MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.

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Report generated on 2026-06-06, 01:26 UTC based on data in: /tmp/nxf.RF6NdpQVby

Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

General Statistics

Showing ⁴⁵⁰/₄₅₀ rows and ¹⁵/₂₄ columns.

Sample Name	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert	≥ 1X	≥ 5X	≥ 10X	≥ 30X	≥ 50X	Median	Vars	SNP	Indel	Ts/Tv	MNP	Multiallelic	Multiallelic SNP	Change rate	Ts/Tv	M Variants
1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1	0.38%	0.0M	426.1M	100.0%	99.4%	3.8%	426.1M	319.2bp	100.0%	100.0%	100.0%	100.0%	99.0%	242X
1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.deconflicted_germline															30497	28440	2057	2.74	0	2	0
1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.deconflicted_germline_custom.ann_snpEff																						99388	2.764	0.03M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1	0.31%	0.0M	1700.2M	100.0%	98.2%	4.3%	1700.2M	293.7bp	100.0%	100.0%	100.0%	100.0%	100.0%	546X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															165	0	91	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						18557667	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															84	0	17	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						33247701	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															7456	0	7456	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						406523	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															16551	16551	0	0.99	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						183133	0.994	0.02M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2	0.32%	0.0M	1076.3M	100.0%	97.8%	4.4%	1076.4M	300.8bp	100.0%	100.0%	100.0%	100.0%	99.0%	402X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															161	0	85	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						17989369	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															81	0	4	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						31135090	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															5987	0	5987	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						506270	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															17461	17461	0	0.93	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						173589	0.929	0.02M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3	0.31%	0.0M	1400.2M	100.0%	98.9%	5.5%	1400.2M	239.4bp	100.0%	100.0%	100.0%	100.0%	100.0%	437X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															155	0	83	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						20072579	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															113	0	16	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						23427977	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															9765	0	9765	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						316259	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															65995	65995	0	1.96	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						46795	1.962	0.07M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4	0.32%	0.0M	1247.7M	100.0%	98.7%	5.5%	1247.8M	248.9bp	100.0%	100.0%	100.0%	100.0%	100.0%	398X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															147	0	77	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						21076208	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															102	0	18	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						25646124	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															9232	0	9232	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						334517	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															67701	67701	0	1.98	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						45616	1.980	0.07M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5	0.35%	0.0M	1224.3M	100.0%	98.5%	7.0%	1224.3M	202.0bp	100.0%	100.0%	100.0%	100.0%	100.0%	317X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															146	0	71	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						21076208	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															129	0	17	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						22488953	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															10358	0	10358	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						298153	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															100857	100857	0	2.40	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						30620	2.402	0.10M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6	0.35%	0.0M	1101.7M	100.0%	98.5%	7.2%	1101.7M	202.6bp	100.0%	100.0%	100.0%	100.0%	100.0%	300X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															140	0	78	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						21696096	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															120	0	19	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						23662624	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															10467	0	10467	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						295048	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															103392	103392	0	2.41	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						29869	2.408	0.10M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7	0.38%	0.0M	1425.2M	100.0%	96.6%	8.3%	1425.2M	176.7bp	100.0%	100.0%	100.0%	100.0%	100.0%	256X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															135	0	67	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						22697454	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															141	0	16	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						18672291	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															11524	0	11524	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						267985	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															125002	125002	0	2.78	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						24705	2.779	0.13M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8	0.39%	0.0M	1167.7M	100.0%	96.5%	8.5%	1167.7M	179.8bp	100.0%	100.0%	100.0%	100.0%	99.0%	235X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															141	0	78	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						21696096	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															140	0	20	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						21006390	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															10929	0	10929	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						282575	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															126422	126422	0	2.78	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						24428	2.775	0.13M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9	0.39%	0.0M	800.3M	100.0%	96.4%	8.8%	800.3M	160.1bp	100.0%	100.0%	100.0%	100.0%	99.0%	208X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															126	0	69	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						24185812	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															93	0	15	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						29195544	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															10875	0	10875	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						283978	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															143440	143440	0	3.01	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						21530	3.012	0.14M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10	0.40%	0.0M	1089.1M	100.0%	96.3%	9.1%	1089.1M	160.4bp	100.0%	100.0%	100.0%	100.0%	99.0%	218X
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															122	0	66	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						24795538	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															89	0	17	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						29926749	0.000	0.00M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															11586	0	11586	0.00	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						266551	0.000	0.01M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															143876	143876	0	3.03	0	0	0
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						21464	3.025	0.14M
1136_5WB-N1-BDNA-1_B23KFG5LT4_1	0.43%	0.0M	258.0M	100.0%	98.8%	3.4%	258.0M	399.6bp	100.0%	100.0%	100.0%	99.0%	97.0%	137X
1136_5WB-N1-BDNA-1_B23KFG5LT4_1.deconflicted_germline															31439	29345	2094	2.73	0	0	0
1136_5WB-N1-BDNA-1_B23KFG5LT4_1.deconflicted_germline_custom.ann_snpEff																						96410	2.744	0.03M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1	0.31%	0.0M	1721.4M	100.0%	98.6%	4.2%	1721.4M	271.9bp	100.0%	100.0%	100.0%	100.0%	99.0%	604X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															204	0	99	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						14827483	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															83	0	19	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						34211023	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															10515	0	10515	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						288258	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															38454	38454	0	1.55	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						78822	1.547	0.04M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2	0.31%	0.0M	2101.8M	100.0%	98.7%	4.2%	2101.8M	269.7bp	100.0%	100.0%	100.0%	100.0%	99.0%	681X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															190	0	90	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						16302039	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															78	0	24	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						32679654	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															11147	0	11147	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						271915	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															38365	38365	0	1.62	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						79005	1.625	0.04M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3	0.33%	0.0M	1348.6M	100.0%	98.8%	5.4%	1348.7M	240.7bp	100.0%	100.0%	100.0%	100.0%	100.0%	449X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															188	0	88	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						16746090	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															82	0	20	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						30255029	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															11914	0	11914	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						259213	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															75931	75931	0	1.98	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						40672	1.978	0.08M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4	0.32%	0.0M	1345.7M	100.0%	98.9%	5.3%	1345.7M	240.6bp	100.0%	100.0%	100.0%	100.0%	100.0%	463X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															183	0	85	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						16484185	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															78	0	14	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						33380637	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															12021	0	12021	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						256906	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															75880	75880	0	1.99	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						40699	1.988	0.08M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5	0.36%	0.0M	1306.4M	100.0%	98.3%	7.2%	1306.4M	198.6bp	100.0%	100.0%	100.0%	100.0%	100.0%	330X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															149	0	67	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						19520379	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															120	0	21	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						23776172	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															12353	0	12353	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						250001	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															98932	98932	0	2.28	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						31216	2.276	0.10M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6	0.36%	0.0M	1296.7M	100.0%	98.4%	7.1%	1296.7M	200.6bp	100.0%	100.0%	100.0%	100.0%	100.0%	324X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															167	0	84	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						17486091	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															127	0	17	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						22045012	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															12231	0	12231	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						252495	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															99703	99703	0	2.29	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						30974	2.289	0.10M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7	0.39%	0.0M	1178.7M	100.0%	96.5%	8.4%	1178.7M	179.5bp	100.0%	100.0%	100.0%	100.0%	99.0%	236X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															151	0	71	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						19402375	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															107	0	14	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						25125512	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															11881	0	11881	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						259933	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															128494	128494	0	2.69	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						24034	2.689	0.13M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8	0.37%	0.0M	1541.8M	100.0%	96.9%	8.1%	1541.8M	174.0bp	100.0%	100.0%	100.0%	100.0%	100.0%	287X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															154	0	74	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						19011723	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															152	0	18	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						18718346	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															13213	0	13213	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						233729	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															118920	118920	0	2.54	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						25969	2.541	0.12M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9	0.39%	0.0M	802.4M	100.0%	96.5%	8.9%	802.4M	160.7bp	100.0%	100.0%	100.0%	100.0%	99.0%	210X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															145	0	69	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						18704115	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															87	0	16	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						31438388	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															11635	0	11635	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						265429	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															140963	140963	0	2.87	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						21908	2.873	0.14M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10	0.38%	0.0M	1506.0M	100.0%	96.7%	8.7%	1506.1M	159.3bp	100.0%	100.0%	100.0%	100.0%	100.0%	262X
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															154	0	71	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						19412296	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															143	0	18	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						19952032	0.000	0.00M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															13721	0	13721	0.00	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						225076	0.000	0.01M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															132911	132911	0	2.80	0	0	0
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						23235	2.797	0.13M
1136_6I8-N1-BDNA-1_B23MHTGLT4_1	0.41%	0.0M	217.6M	100.0%	98.5%	3.6%	217.6M	389.0bp	100.0%	100.0%	100.0%	100.0%	98.0%	136X
1136_6I8-N1-BDNA-1_B23MHTGLT4_1.deconflicted_germline															31159	29038	2121	2.68	0	0	0
1136_6I8-N1-BDNA-1_B23MHTGLT4_1.deconflicted_germline_custom.ann_snpEff																						99113	2.717	0.03M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1	0.32%	0.0M	1961.6M	100.0%	98.2%	4.5%	1961.6M	288.8bp	100.0%	100.0%	100.0%	100.0%	100.0%	577X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															162	0	91	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						19682093	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															102	0	14	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						27594969	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															9427	0	9427	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						327598	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															20114	20114	0	1.10	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						153538	1.096	0.02M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2	0.32%	0.0M	1281.1M	100.0%	98.3%	4.5%	1281.1M	286.5bp	100.0%	100.0%	100.0%	100.0%	100.0%	491X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															161	0	92	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						19036575	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															66	0	12	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						40452567	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															8270	0	8270	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						373430	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															20226	20226	0	0.98	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						152688	0.985	0.02M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3	0.33%	0.0M	1583.9M	100.0%	98.8%	5.7%	1583.9M	240.5bp	100.0%	100.0%	100.0%	100.0%	100.0%	470X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															138	0	84	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						22185482	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															95	0	19	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						25387804	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															11661	0	11661	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						264837	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															68180	68180	0	1.90	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						45295	1.895	0.07M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4	0.33%	0.0M	1362.9M	100.0%	98.7%	5.7%	1362.9M	242.7bp	100.0%	100.0%	100.0%	100.0%	100.0%	428X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															151	0	94	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						20619336	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															88	0	17	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						28815016	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															11184	0	11184	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						276132	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															68655	68655	0	1.88	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						44982	1.875	0.07M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5	0.36%	0.0M	1123.9M	100.0%	98.3%	7.3%	1123.9M	205.2bp	100.0%	100.0%	100.0%	100.0%	100.0%	286X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															131	0	78	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						21502918	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															87	0	13	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						28757883	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															11623	0	11623	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						265703	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															102784	102784	0	2.29	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						30046	2.286	0.10M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6	0.36%	0.0M	1086.9M	100.0%	98.3%	7.2%	1086.9M	202.4bp	100.0%	100.0%	100.0%	100.0%	100.0%	299X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															139	0	80	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						22019918	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															117	0	14	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						21539066	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															11669	0	11669	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						264655	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															103229	103229	0	2.28	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						29916	2.284	0.10M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7	0.36%	0.0M	1235.2M	100.0%	97.4%	7.7%	1235.2M	173.8bp	100.0%	100.0%	100.0%	100.0%	100.0%	303X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															127	0	75	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						23418008	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															119	0	11	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						23767155	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															13112	0	13112	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						235530	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															112586	112586	0	2.47	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						27430	2.466	0.11M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8	0.37%	0.0M	1029.8M	100.0%	97.3%	7.9%	1029.8M	177.0bp	100.0%	100.0%	100.0%	100.0%	100.0%	278X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															138	0	78	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						22019918	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															101	0	12	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						27430864	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															12389	0	12389	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						249275	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															116279	116279	0	2.54	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						26559	2.536	0.12M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9	0.39%	0.0M	940.9M	100.0%	96.5%	8.7%	940.9M	162.8bp	100.0%	100.0%	100.0%	100.0%	99.0%	212X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															116	0	69	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						24574764	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															92	0	13	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						26837721	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															12197	0	12197	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						253199	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															142530	142530	0	2.81	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						21667	2.807	0.14M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10	0.39%	0.0M	1036.8M	100.0%	96.6%	8.7%	1036.9M	162.5bp	100.0%	100.0%	100.0%	100.0%	99.0%	218X
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															123	0	72	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						22936446	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															101	0	6	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						29239986	0.000	0.00M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															12491	0	12491	0.00	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						247239	0.000	0.01M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															140613	140613	0	2.87	0	0	0
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						21962	2.867	0.14M
1136_85O-N1-BDNA-1_B23KGCJLT4_1	0.44%	0.0M	212.2M	100.0%	99.3%	3.6%	212.2M	367.6bp	100.0%	100.0%	100.0%	99.0%	96.0%	118X
1136_85O-N1-BDNA-1_B23KGCJLT4_1.deconflicted_germline															30777	28745	2032	2.75	0	0	0
1136_85O-N1-BDNA-1_B23KGCJLT4_1.deconflicted_germline_custom.ann_snpEff																						98484	2.775	0.03M
1136_85O-T1-TDNA-1_A23WJ5GLT4_1	0.31%	0.0M	1477.1M	100.0%	98.8%	4.6%	1477.1M	234.2bp	100.0%	100.0%	100.0%	100.0%	99.0%	416X
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															145	0	82	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						21227835	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															210	0	5	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						14433535	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															9534	0	9534	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						317919	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															37563	37563	0	2.05	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						80692	2.048	0.04M
1136_85O-T1-TDNA-1_A23WJ5GLT4_2	0.31%	0.0M	1257.2M	100.0%	98.8%	4.6%	1257.3M	235.1bp	100.0%	100.0%	100.0%	100.0%	99.0%	407X
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															139	0	80	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						21856808	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															167	0	7	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						17484360	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															9280	0	9280	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						326620	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															37014	37014	0	2.04	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						81889	2.043	0.04M
1136_85O-T1-TDNA-1_A23WJ5GLT4_3	0.34%	0.0M	990.6M	100.0%	98.7%	6.2%	990.6M	201.1bp	100.0%	100.0%	100.0%	100.0%	100.0%	307X
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															131	0	74	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						23680018	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															101	0	7	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						26952394	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															10940	0	10940	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						282291	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															103282	103282	0	2.54	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						29901	2.545	0.10M
1136_85O-T1-TDNA-1_A23WJ5GLT4_4	0.35%	0.0M	1016.0M	100.0%	98.6%	6.3%	1016.0M	208.2bp	100.0%	100.0%	100.0%	100.0%	100.0%	283X
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															119	0	65	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						24494536	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															116	0	10	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						24292216	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															10706	0	10706	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						288461	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															105516	105516	0	2.60	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						29268	2.597	0.11M
1136_85O-T1-TDNA-1_A23WJ5GLT4_5	0.37%	0.0M	1200.7M	100.0%	97.8%	7.9%	1200.8M	170.2bp	100.0%	100.0%	100.0%	100.0%	100.0%	260X
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															115	0	64	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						25842859	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															135	0	17	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						21510808	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															12432	0	12432	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						248412	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															132759	132759	0	2.91	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						23262	2.915	0.13M
1136_85O-T1-TDNA-1_A23WJ5GLT4_6	0.38%	0.0M	1151.8M	100.0%	97.7%	8.1%	1151.8M	171.4bp	100.0%	100.0%	100.0%	100.0%	100.0%	238X
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															125	0	69	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						23747909	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															121	0	12	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						22568674	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															12174	0	12174	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						253677	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															136219	136219	0	2.97	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						22671	2.965	0.14M
1136_85O-T1-TDNA-1_A23WJ5GLT4_7	0.38%	0.0M	1322.1M	100.0%	97.6%	8.4%	1322.1M	156.3bp	100.0%	100.0%	100.0%	100.0%	100.0%	257X
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															104	0	56	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						28153889	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															125	0	9	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						23244687	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															13443	0	13443	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						229730	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															143900	143900	0	3.08	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						21461	3.084	0.14M
1136_85O-T1-TDNA-1_A23WJ5GLT4_8	0.38%	0.0M	810.6M	100.0%	97.6%	8.5%	810.7M	156.9bp	100.0%	100.0%	100.0%	100.0%	99.0%	216X
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															111	0	62	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						27077056	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															79	0	5	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						33352054	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															12016	0	12016	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						257013	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															155988	155988	0	3.14	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19798	3.141	0.16M
1136_85O-T1-TDNA-1_A23WJ5GLT4_9	0.39%	0.0M	1085.9M	100.0%	98.0%	8.8%	1085.9M	146.7bp	100.0%	100.0%	100.0%	100.0%	99.0%	232X
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															112	0	64	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						27852560	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															114	0	12	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						25019595	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															13122	0	13122	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						235350	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															156056	156056	0	3.19	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19789	3.189	0.16M
1136_85O-T1-TDNA-1_A23WJ5GLT4_10	0.38%	0.0M	1353.2M	100.0%	98.0%	8.8%	1353.2M	147.0bp	100.0%	100.0%	100.0%	100.0%	99.0%	240X
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															111	0	66	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						26580229	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															123	0	16	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						21470524	0.000	0.00M
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															13865	0	13865	0.00	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						222738	0.000	0.01M
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															155012	155012	0	3.19	0	0	0
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19922	3.186	0.16M
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1	0.32%	0.0M	3057.7M	100.0%	97.5%	3.6%	3057.8M	356.9bp	100.0%	100.0%	100.0%	100.0%	100.0%	1352X
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.diploid_sv															222	0	108	0.00	0	0	0
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.diploid_sv_custom.ann_snpEff																						13473375	0.000	0.00M
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv															332	0	183	0.00	0	0	0
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff																						9240982	0.000	0.00M
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_indels															32305	0	32305	0.00	0	0	0
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						95597	0.000	0.03M
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_snvs															189936	189936	0	2.34	0	0	0
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						16259	2.341	0.19M
NA12878_c_0002_gDNA_0005_B23KYWJLT4_1	0.38%	0.0M	347.6M	100.0%	99.0%	3.8%	347.6M	304.9bp	100.0%	100.0%	100.0%	99.0%	99.0%	207X
NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconflicted_germline															31237	29143	2094	2.70	0	0	0
NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconflicted_germline_custom.ann_snpEff																						98865	2.740	0.03M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1	0.41%	0.0M	1130.9M	100.0%	98.7%	9.6%	1130.9M	141.1bp	100.0%	100.0%	100.0%	100.0%	99.0%	189X
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															124	0	65	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						24588909	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															121	0	23	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						23091883	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															12422	0	12422	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						248612	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															161696	161696	0	3.21	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19099	3.210	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															124	0	60	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						23089112	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															119	0	21	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						23052936	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															13192	0	13192	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						234101	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															164035	164035	0	3.14	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						18826	3.142	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															113	0	70	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						27070359	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															124	0	15	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						23657370	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															13340	0	13340	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						231504	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															164633	164633	0	3.14	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						18758	3.143	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															96	0	58	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						31905709	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															113	0	13	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						24726706	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															13203	0	13203	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						233906	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															163023	163023	0	3.16	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						18943	3.157	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2	0.41%	0.0M	900.6M	100.0%	98.7%	9.5%	900.6M	141.1bp	100.0%	100.0%	100.0%	100.0%	99.0%	189X
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															125	0	62	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						24185812	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															102	0	26	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						25975323	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															11915	0	11915	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						259191	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															159051	159051	0	3.17	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19416	3.174	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv															129	0	60	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff																						21833033	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv															96	0	19	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff																						29276639	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels															12647	0	12647	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff																						244189	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs															161306	161306	0	3.11	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19145	3.111	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv															111	0	65	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff																						27576347	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv															91	0	13	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff																						30885245	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels															12856	0	12856	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff																						240220	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs															161780	161780	0	3.11	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19089	3.106	0.16M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv															98	0	60	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff																						30736136	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv															83	0	14	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff																						32484253	0.000	0.00M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels															12650	0	12650	0.00	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff																						244132	0.000	0.01M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs															160264	160264	0	3.12	0	0	0
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff																						19269	3.120	0.16M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools Flagstat: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_flagstat_stats-error_rate`
\|\|	Samtools Flagstat: stats	Non-primary	Non-primary alignments (millions)	`samtools_flagstat_stats-non_primary_alignments`	read_count
\|\|	Samtools Flagstat: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_flagstat_stats-reads_mapped`	read_count
\|\|	Samtools Flagstat: stats	% Mapped	% Mapped reads	`samtools_flagstat_stats-reads_mapped_percent`
\|\|	Samtools Flagstat: stats	% Proper pairs	% Properly paired reads	`samtools_flagstat_stats-reads_properly_paired_percent`
\|\|	Samtools Flagstat: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_flagstat_stats-reads_MQ0_percent`
\|\|	Samtools Flagstat: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_flagstat_stats-raw_total_sequences`	read_count
\|\|	Samtools Flagstat: stats	Mean insert	Average insert size	`samtools_flagstat_stats-insert_size_average`
\|\|	Mosdepth	≥ 1X	Fraction of genome with at least 1X coverage	`mosdepth-1_x_pc`
\|\|	Mosdepth	≥ 5X	Fraction of genome with at least 5X coverage	`mosdepth-5_x_pc`
\|\|	Mosdepth	≥ 10X	Fraction of genome with at least 10X coverage	`mosdepth-10_x_pc`
\|\|	Mosdepth	≥ 30X	Fraction of genome with at least 30X coverage	`mosdepth-30_x_pc`
\|\|	Mosdepth	≥ 50X	Fraction of genome with at least 50X coverage	`mosdepth-50_x_pc`
\|\|	Mosdepth	Median	Median coverage	`mosdepth-median_coverage`
\|\|	Bcftools: Stats	Vars	Variations total	`bcftools_stats-number_of_records`
\|\|	Bcftools: Stats	SNP	Variation SNPs	`bcftools_stats-number_of_SNPs`
\|\|	Bcftools: Stats	Indel	Variation Insertions/Deletions	`bcftools_stats-number_of_indels`
\|\|	Bcftools: Stats	Ts/Tv	Variant SNP transition / transversion ratio	`bcftools_stats-tstv`
\|\|	Bcftools: Stats	MNP	Variation multinucleotide polymorphisms	`bcftools_stats-number_of_MNPs`
\|\|	Bcftools: Stats	Multiallelic	Variation sites with multiple alleles	`bcftools_stats-number_of_multiallelic_sites`
\|\|	Bcftools: Stats	Multiallelic SNP	Variation sites with multiple SNPs	`bcftools_stats-number_of_multiallelic_SNP_sites`
\|\|	SNPeff	Change rate	Change rate	`snpeff-Change_rate`
\|\|	SNPeff	Ts/Tv	Transitions / Transversions ratio	`snpeff-Ts_Tv_ratio`
\|\|	SNPeff	M Variants	Number of variants before filter (millions)	`snpeff-Number_of_variants_before_filter`

altera/sarek Workflow Summary

this information is collected when the pipeline is started.https://github.com/altera/sarek

Input/output options

input: s3://natera-platform-sandbox/platform-users/sgreer/samplesheets/samplesheet_sarek_cgp_dna_exp0035.csv
outdir: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0035/tools__44c19e3d--20260605-213512

Main options

hrd_coverage_profile: s3://natera-platform-sandbox/pipeline-resources/AIH/hrd_score_altera_bam/dbsnp_baseline_altera.260120.tsv.gz
intervals_dir: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals
intervals_vc_dir: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_padded_intervals
mimsi_microsatellites_list: s3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv
mimsi_model: s3://natera-platform-sandbox/pipeline-resources/mimsi/mi_msi_v0_4_0_200x_attn.model
tools: ngscheckmate,contamination,tnseq,strelka,manta,msisensor2,mimsi,cnvkit,facets,hla_optitype,tmb,hrd,whatshap,snpeff,merge,sentieon_haplotyper_rf,chip_detection,germline_cnv,snv_indel,sex_estimation
wes: true

Variant Calling

chip_cohort_blacklist: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cohort_blacklist.bed.gz
chip_cosmic_heme: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cosmic_heme.tsv.gz
chip_encode_blacklist: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/encode_blacklist.bed.gz
chip_gene_family_blacklist: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_family_blacklist.bed.gz
chip_gene_tiers: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_tiers.tsv
chip_pon: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz
chip_pon_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz.tbi
cnvkit_reference: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/cnvkit/cnvkit_wes_altera.reference.cnn
pon: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
pon_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi
pot: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
pot_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz.tbi

General reference genome options

igenomes_base: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/
optitype_reference: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/optitype/original_v3.15_2014/

Reference genome options

blacklist_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_grch38.bed.gz
blacklist_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_grch38.bed.gz.tbi
blacklist_header: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_header.txt
conpair_markers: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Conpair/GRCh38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.liftover.bed
container_registry_seqera: 292967571998.dkr.ecr.us-west-2.amazonaws.com/community.wave.seqera.io
dbsnp: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
dbsnp_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
dbsnp_vqsr: --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
dict: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
exome_bed: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed
fasta: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
fasta_fai: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
genome_annotations: s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz
germline_rescue_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed
germline_resource: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
germline_resource_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
gt_correction_model: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/gt_correction_model_v2.joblib
gt_correction_threshold_grch38: 0.5
lowdepth_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz
lowdepth_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz.tbi
lowdepth_header: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_header.txt
ngscheckmate_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
probe_bed: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
repeatmasker_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz
repeatmasker_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz.tbi
repeatmasker_header: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_header.txt
rf_blacklist_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz
rf_blacklist_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz.tbi
rf_boosted_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz
rf_boosted_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz.tbi
rf_indel_fp_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz
rf_indel_fp_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz.tbi
rf_indel_fp_rates_tsv: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_locus_fp_rates.tsv
rf_indel_model: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_rf_model_v7.joblib
rf_low_depth_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz
rf_low_depth_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz.tbi
rf_repeatmasker_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz
rf_repeatmasker_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz.tbi
rf_snv_fp_bed: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz
rf_snv_fp_bed_tbi: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz.tbi
rf_snv_model: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_rf_model_v4.joblib
snpeff_cache: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/annotation-cache/snpeff_cache/
snpeff_db: GRCh38.105
target_beds: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/foresight_clarity_targets_hg38.bed
vep_cache: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/annotation-cache/vep_cache/
vep_cache_version: 113
vep_genome: GRCh38
vep_species: homo_sapiens

Institutional config options

modules_testdata_base_path: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/

Low reads filtering

min_mapped_reads_normal: 25000000
min_mapped_reads_tumor: 50000000

Generic options

task_job_queue: Nextflow-OnDemand

Core Nextflow options

configFiles: N/A
container: [GERMLINE_CNV:292967571998.dkr.ecr.us-west-2.amazonaws.com/sarek/altera_cnv:0.5.0, SOMA_CNV_PROBE_COUNTS|SOMA_CNV_ALLELE_COUNTS|SOMA_CNV_NORMALIZE|SOMA_CNV_BUILD_REFERENCE|SOMA_CNV_CALL|SOMA_CNV_EXPORT_VIEWER|SOMA_CNV_BGZIP_TABIX:292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-3cb5ec5]
containerEngine: docker
launchDir: /code
profile: eks,docker,std_run
projectDir: /tmp/home/.nextflow/assets/rd-platform/bioinformatics/nextflow/sarek
runName: sarek-cgp-dna-exp0035-tools-20260605-213512
userName: nextflow
workDir: /natera-rnd-pltf-dev-nextflow-scratch-01/work

Samtools Flagstat

Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

This module parses the output from samtools stats. All numbers in millions.

Created with MultiQC

Showing ⁴⁸/₄₈ rows and ¹³/₁₃ columns.

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1	426.1M	426.0M	423.6M	170.2M	0.0M	16.0M	62453.7Mb	0.0Mb	25160.6Mb	1.1M	0.0M	198.6M	13.3M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1	1700.2M	1700.2M	1669.7M	1224.8M	0.0M	72.8M	245352.9Mb	0.0Mb	176492.1Mb	13.7M	0.8M	755.4M	80.3M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2	1076.4M	1076.3M	1052.6M	723.7M	0.0M	46.8M	155460.1Mb	0.0Mb	104399.7Mb	10.7M	0.6M	477.6M	49.3M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3	1400.2M	1400.2M	1384.7M	992.4M	0.0M	77.1M	194808.4Mb	0.0Mb	137959.5Mb	6.7M	0.4M	582.1M	110.9M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4	1247.8M	1247.7M	1232.1M	872.6M	0.0M	69.2M	174612.1Mb	0.0Mb	122164.4Mb	6.9M	0.4M	523.2M	93.3M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5	1224.3M	1224.2M	1205.6M	884.4M	0.0M	86.1M	164021.8Mb	0.0Mb	118593.5Mb	5.3M	0.4M	473.0M	133.4M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6	1101.7M	1101.7M	1084.7M	777.3M	0.0M	79.6M	147487.3Mb	0.0Mb	104215.7Mb	4.9M	0.4M	423.9M	121.7M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7	1425.2M	1425.2M	1376.9M	1098.9M	0.0M	118.6M	186271.4Mb	0.0Mb	143898.6Mb	6.5M	0.7M	519.5M	185.9M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8	1167.7M	1167.7M	1126.6M	869.7M	0.0M	98.9M	153243.7Mb	0.0Mb	114432.4Mb	5.7M	0.6M	427.9M	149.7M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9	800.3M	800.3M	771.8M	541.3M	0.0M	70.1M	103004.1Mb	0.0Mb	69775.0Mb	3.3M	0.4M	282.4M	114.1M
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10	1089.1M	1089.1M	1049.0M	797.4M	0.0M	99.3M	140087.0Mb	0.0Mb	102821.5Mb	4.8M	0.5M	383.9M	155.3M
1136_5WB-N1-BDNA-1_B23KFG5LT4_1	258.0M	258.0M	255.0M	106.7M	0.0M	8.8M	38276.6Mb	0.0Mb	15952.9Mb	1.4M	0.1M	122.4M	5.2M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1	1721.4M	1721.4M	1697.4M	1222.1M	0.0M	72.7M	247007.1Mb	0.0Mb	174697.4Mb	10.7M	0.6M	756.0M	93.4M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2	2101.8M	2101.7M	2074.7M	1538.9M	0.0M	88.3M	301607.6Mb	0.0Mb	220063.5Mb	12.0M	0.6M	923.6M	114.6M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3	1348.7M	1348.6M	1333.0M	943.8M	0.0M	72.9M	188345.3Mb	0.0Mb	131646.2Mb	6.8M	0.4M	562.1M	105.0M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4	1345.7M	1345.7M	1330.5M	930.1M	0.0M	72.0M	187717.4Mb	0.0Mb	129680.7Mb	6.6M	0.4M	560.9M	104.9M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5	1306.4M	1306.4M	1284.5M	953.0M	0.0M	94.1M	174769.2Mb	0.0Mb	127586.6Mb	5.8M	0.4M	500.8M	146.2M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6	1296.7M	1296.7M	1275.6M	950.2M	0.0M	92.0M	174322.4Mb	0.0Mb	127861.7Mb	5.8M	0.4M	499.7M	142.5M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7	1178.7M	1178.7M	1137.9M	886.4M	0.0M	99.4M	154945.3Mb	0.0Mb	116798.6Mb	5.7M	0.5M	432.9M	150.2M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8	1541.8M	1541.8M	1494.5M	1188.7M	0.0M	125.0M	201028.9Mb	0.0Mb	155160.8Mb	6.2M	0.7M	560.5M	203.5M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9	802.4M	802.4M	774.4M	544.4M	0.0M	71.3M	103430.9Mb	0.0Mb	70264.7Mb	3.3M	0.4M	283.8M	113.8M
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10	1506.1M	1506.0M	1456.6M	1161.2M	0.0M	131.2M	193487.2Mb	0.0Mb	149423.6Mb	5.7M	0.7M	530.7M	215.9M
1136_6I8-N1-BDNA-1_B23MHTGLT4_1	217.6M	217.6M	214.3M	71.9M	0.0M	7.9M	32164.7Mb	0.0Mb	10736.0Mb	1.5M	0.1M	102.3M	4.9M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1	1961.6M	1961.5M	1925.5M	1468.5M	0.0M	88.7M	282758.0Mb	0.0Mb	211315.8Mb	16.3M	0.8M	867.8M	95.8M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2	1281.1M	1281.1M	1258.7M	866.4M	0.0M	58.3M	184579.9Mb	0.0Mb	124653.1Mb	10.1M	0.5M	566.7M	63.2M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3	1583.9M	1583.9M	1564.4M	1148.0M	0.0M	90.0M	220337.1Mb	0.0Mb	159624.4Mb	8.5M	0.5M	658.3M	124.6M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4	1362.9M	1362.9M	1345.3M	967.4M	0.0M	77.4M	190137.1Mb	0.0Mb	134964.1Mb	7.7M	0.5M	567.9M	105.3M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5	1123.9M	1123.9M	1104.5M	812.7M	0.0M	81.7M	151540.2Mb	0.0Mb	109773.6Mb	5.8M	0.4M	434.8M	120.9M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6	1086.9M	1086.9M	1068.9M	767.8M	0.0M	78.0M	146180.1Mb	0.0Mb	103413.9Mb	5.1M	0.4M	419.9M	118.0M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7	1235.2M	1235.2M	1203.6M	889.1M	0.0M	95.4M	161774.1Mb	0.0Mb	116520.9Mb	4.3M	0.5M	451.7M	161.1M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8	1029.8M	1029.8M	1001.9M	713.5M	0.0M	81.8M	135132.8Mb	0.0Mb	93770.6Mb	3.9M	0.4M	378.5M	132.0M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9	940.9M	940.9M	908.1M	672.6M	0.0M	81.7M	121762.9Mb	0.0Mb	87218.5Mb	4.0M	0.4M	334.6M	131.4M
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10	1036.9M	1036.8M	1001.2M	756.7M	0.0M	90.1M	134119.8Mb	0.0Mb	98076.3Mb	4.3M	0.5M	368.4M	145.2M
1136_85O-N1-BDNA-1_B23KGCJLT4_1	212.2M	212.2M	210.8M	83.9M	0.0M	7.6M	31422.5Mb	0.0Mb	12520.8Mb	0.6M	0.0M	100.5M	4.9M
1136_85O-T1-TDNA-1_A23WJ5GLT4_1	1477.1M	1477.1M	1459.5M	1087.9M	0.0M	67.7M	208004.5Mb	0.0Mb	152582.6Mb	7.0M	0.7M	624.5M	106.3M
1136_85O-T1-TDNA-1_A23WJ5GLT4_2	1257.3M	1257.2M	1242.6M	879.5M	0.0M	57.3M	177410.9Mb	0.0Mb	123710.1Mb	5.8M	0.6M	533.7M	88.5M
1136_85O-T1-TDNA-1_A23WJ5GLT4_3	990.6M	990.6M	978.0M	677.5M	0.0M	61.1M	134420.9Mb	0.0Mb	91780.8Mb	4.1M	0.4M	390.3M	100.5M
1136_85O-T1-TDNA-1_A23WJ5GLT4_4	1016.0M	1016.0M	1002.1M	719.6M	0.0M	64.3M	138574.4Mb	0.0Mb	98121.2Mb	4.9M	0.5M	403.9M	98.8M
1136_85O-T1-TDNA-1_A23WJ5GLT4_5	1200.8M	1200.7M	1173.9M	886.6M	0.0M	95.2M	156911.1Mb	0.0Mb	115889.3Mb	4.6M	0.5M	438.3M	157.0M
1136_85O-T1-TDNA-1_A23WJ5GLT4_6	1151.8M	1151.8M	1124.8M	855.6M	0.0M	93.7M	150755.5Mb	0.0Mb	112139.7Mb	4.8M	0.5M	421.1M	149.6M
1136_85O-T1-TDNA-1_A23WJ5GLT4_7	1322.1M	1322.1M	1290.7M	993.6M	0.0M	111.4M	169766.8Mb	0.0Mb	127624.8Mb	4.5M	0.5M	465.7M	190.2M
1136_85O-T1-TDNA-1_A23WJ5GLT4_8	810.7M	810.6M	791.0M	547.1M	0.0M	68.9M	104563.8Mb	0.0Mb	70554.6Mb	2.9M	0.3M	286.4M	115.7M
1136_85O-T1-TDNA-1_A23WJ5GLT4_9	1085.9M	1085.9M	1064.5M	785.7M	0.0M	95.7M	137343.9Mb	0.0Mb	99323.7Mb	3.5M	0.4M	371.9M	167.1M
1136_85O-T1-TDNA-1_A23WJ5GLT4_10	1353.2M	1353.1M	1325.9M	1029.1M	0.0M	119.0M	171458.4Mb	0.0Mb	130413.2Mb	4.3M	0.5M	464.1M	207.7M
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1	3057.8M	3057.7M	2982.5M	1831.1M	0.0M	109.0M	450336.3Mb	0.0Mb	269186.6Mb	34.7M	1.3M	1407.4M	85.5M
NA12878_c_0002_gDNA_0005_B23KYWJLT4_1	347.6M	347.6M	344.0M	131.8M	0.0M	13.1M	50971.2Mb	0.0Mb	19490.9Mb	1.6M	0.1M	160.4M	11.8M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1	1130.9M	1130.9M	1116.3M	859.8M	0.0M	108.7M	142641.6Mb	0.0Mb	108602.5Mb	4.0M	0.4M	382.3M	178.8M
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2	900.6M	900.6M	889.2M	639.5M	0.0M	85.6M	113608.2Mb	0.0Mb	80753.7Mb	3.2M	0.3M	303.6M	143.2M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

Mosdepth

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.https://github.com/brentp/mosdepthDOI: 10.1093/bioinformatics/btx699

Cumulative coverage distribution

Proportion of bases in the reference genome with, at least, a given depth of coverage. Note that for 48 samples, a BED file was provided, so the data was calculated across those regions. For 48 samples, it's calculated across the entire genome length. 48 samples have both global and region reports, and we are showing the data for regions

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

Created with MultiQC

Average coverage per contig

Average coverage per contig or chromosome

Created with MultiQC

XY coverage

Created with MultiQC

Bcftools

Utilities for variant calling and manipulating VCFs and BCFs.https://samtools.github.io/bcftoolsDOI: 10.1093/gigascience/giab008

Variant Substitution Types

Created with MultiQC

Variant Quality

Created with MultiQC

Indel Distribution

Created with MultiQC

Variant depths

Read depth support distribution for called variants

Created with MultiQC

Vcftools

Program to analyse and reporting on VCF files.https://vcftools.github.ioDOI: 10.1093/bioinformatics/btr330

TsTv by Count

Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.

Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Alternative allele count is the number of alternative alleles at the site. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-count

Created with MultiQC

TsTv by Qual

Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

Created with MultiQC

SNPeff

Annotates and predicts the effects of variants on genes (such as amino acid changes).http://snpeff.sourceforge.netDOI: 10.4161/fly.19695

Variants by Genomic Region

The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

Created with MultiQC

Variant Effects by Impact

The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

There are four levels of impacts predicted by SnpEff:

High: High impact (like stop codon)
Moderate: Middle impact (like same type of amino acid substitution)
Low: Low impact (ie silence mutation)
Modifier: No impact

Created with MultiQC

Variants by Effect Types

The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

This plot shows the effect of variants with respect to the mRNA.

Created with MultiQC

Variants by Functional Class

The stacked bar plot shows the effect of variants and the number of variants for each effect type.

This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

Silent: The amino acid does not change.
Missense: The amino acid is different.
Nonsense: The variant generates a stop codon.

Created with MultiQC

Variant Qualities

The line plot shows the quantity as function of the variant quality score.

The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

Created with MultiQC

VEP

Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.https://www.ensembl.org/info/docs/tools/vep/index.htmlDOI: 10.1186/s13059-016-0974-4

General Statistics

Table showing general statistics of VEP annotation run

Showing ²⁰¹/₂₀₁ rows and ⁷/₈ columns.

Sample Name	Overlapped regulatory features	Overlapped transcripts	Overlapped genes	Existing variants	Variants processed	Lines of input read
1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.deconflicted_germline_custom.ann_snpEff_VEP.ann	1018	17600	16983	30497	30497	30497
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	52	242	242	165	165	165
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	9	79	79	84	84	84
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	476	8465	8326	7456	7456	7456
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	877	13536	13187	16551	16551	16551
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	47	250	250	161	161	161
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	2	66	66	81	81	81
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	373	7152	7059	5987	5987	5987
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	990	14868	14458	17461	17461	17461
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	29	215	215	155	155	155
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	8	91	91	113	113	113
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	674	10309	10110	9765	9765	9765
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	3285	27749	26231	65995	65995	65995
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	65	233	233	147	147	147
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	3	100	100	102	102	102
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	594	9858	9692	9232	9232	9232
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	3303	28010	26460	67701	67701	67701
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	32	200	200	146	146	146
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	13	124	124	129	129	129
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	703	10735	10521	10358	10358	10358
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5111	32310	30229	100857	100857	100857
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	31	205	205	140	140	140
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	7	99	99	120	120	120
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	710	10723	10495	10467	10467	10467
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5096	32398	30302	103392	103392	103392
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	148	271	271	135	135	135
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	4	134	133	141	141	141
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	784	11403	11141	11524	11524	11524
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6301	34310	31918	125002	125002	125002
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	50	215	215	141	141	141
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	44	142	142	140	140	140
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	755	10987	10745	10929	10929	10929
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6218	34310	31926	126422	126422	126422
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	41	188	188	126	126	126
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	12	100	100	93	93	93
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	698	11028	10789	10875	10875	10875
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6963	35432	32920	143440	143440	143440
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	35	185	185	122	122	122
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	8	90	89	89	89	89
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	732	11365	11109	11586	11586	11586
1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6945	35335	32802	143876	143876	143876
1136_5WB-N1-BDNA-1_B23KFG5LT4_1.deconflicted_germline_custom.ann_snpEff_VEP.ann	1083	17801	17182	31439	31439	31439
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	59	300	299	204	204	204
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	10	89	89	83	83	83
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	734	11004	10774	10515	10515	10515
1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	1783	20566	19677	38454	38454	38454
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	55	292	292	190	190	190
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	15	80	80	78	78	78
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	760	11305	11076	11147	11147	11147
1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	1774	20344	19494	38365	38365	38365
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	70	298	297	188	188	188
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	9	88	88	82	82	82
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	844	11922	11666	11914	11914	11914
1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	3260	28634	27035	75931	75931	75931
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	62	251	251	183	183	183
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	6	58	58	78	78	78
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	834	12090	11817	12021	12021	12021
1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	3261	28573	26974	75880	75880	75880
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	51	229	229	149	149	149
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	305	162	162	120	120	120
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	857	12130	11833	12353	12353	12353
1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	4444	31776	29767	98932	98932	98932
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	68	253	253	167	167	167
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	12	118	118	127	127	127
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	866	12083	11807	12231	12231	12231
1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	4529	31934	29944	99703	99703	99703
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	47	230	230	151	151	151
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	30	145	145	107	107	107
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	838	11775	11530	11881	11881	11881
1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5960	34624	32193	128494	128494	128494
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	47	240	240	154	154	154
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	29	149	149	152	152	152
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	922	12546	12244	13213	13213	13213
1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5493	33733	31436	118920	118920	118920
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	64	227	227	145	145	145
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	8	103	103	87	87	87
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	790	11563	11311	11635	11635	11635
1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6578	35396	32829	140963	140963	140963
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	63	234	234	154	154	154
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	13	171	171	143	143	143
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	919	12789	12468	13721	13721	13721
1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6411	34827	32420	132911	132911	132911
1136_6I8-N1-BDNA-1_B23MHTGLT4_1.deconflicted_germline_custom.ann_snpEff_VEP.ann	1075	17465	16839	31159	31159	31159
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	54	243	243	162	162	162
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	3	89	89	102	102	102
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	668	10153	9966	9427	9427	9427
1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	973	14758	14355	20114	20114	20114
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	55	245	245	161	161	161
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	4	72	72	66	66	66
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	558	9199	9036	8270	8270	8270
1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	1010	15193	14778	20226	20226	20226
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	39	193	193	138	138	138
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	8	101	101	95	95	95
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	807	11842	11597	11661	11661	11661
1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	3215	27833	26308	68180	68180	68180
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	50	231	231	151	151	151
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	24	98	98	88	88	88
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	793	11309	11075	11184	11184	11184
1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	3232	27903	26409	68655	68655	68655
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	27	192	192	131	131	131
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	21	105	105	87	87	87
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	821	11763	11497	11623	11623	11623
1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	4992	32428	30357	102784	102784	102784
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	39	205	205	139	139	139
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	22	103	103	117	117	117
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	799	11778	11535	11669	11669	11669
1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5149	32615	30512	103229	103229	103229
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	26	181	181	127	127	127
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	30	125	124	119	119	119
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	939	12645	12355	13112	13112	13112
1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5511	33389	31174	112586	112586	112586
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	31	205	205	138	138	138
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	26	112	111	101	101	101
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	839	12274	11999	12389	12389	12389
1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5714	33602	31343	116279	116279	116279
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	46	181	181	116	116	116
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	25	93	93	92	92	92
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	845	12078	11822	12197	12197	12197
1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6844	35443	32906	142530	142530	142530
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	33	189	189	123	123	123
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	22	124	124	101	101	101
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	850	12215	11927	12491	12491	12491
1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6801	35413	32872	140613	140613	140613
1136_85O-N1-BDNA-1_B23KGCJLT4_1.deconflicted_germline_custom.ann_snpEff_VEP.ann	1081	17516	16894	30777	30777	30777
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	27	199	199	144	144	145
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	8	159	158	210	210	210
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	581	9820	9633	9534	9534	9534
1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	2017	22595	21705	37563	37563	37563
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	27	205	205	138	138	139
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	3	119	119	167	167	167
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	532	9717	9535	9280	9280	9280
1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	2042	22397	21478	37014	37014	37014
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	22	189	189	130	130	131
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	160	135	135	101	101	101
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	721	11195	10972	10940	10940	10940
1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5156	32620	30564	103282	103282	103282
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	19	161	161	118	118	119
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	21	108	108	116	116	116
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	717	10948	10735	10706	10706	10706
1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	5272	32689	30556	105516	105516	105516
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	18	161	161	115	115	115
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	26	152	152	134	134	135
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	839	12271	11966	12432	12432	12432
1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6562	34726	32304	132759	132759	132759
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	19	160	160	125	125	125
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	24	104	104	121	121	121
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	807	12033	11757	12174	12174	12174
1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	6611	34855	32392	136219	136219	136219
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	22	149	149	104	104	104
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	26	128	127	125	125	125
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	915	12712	12405	13443	13443	13443
1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7058	35491	32981	143900	143900	143900
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	20	163	163	111	111	111
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	20	82	82	79	79	79
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	780	11945	11676	12016	12016	12016
1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7332	35994	33382	155988	155988	155988
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	17	157	157	112	112	112
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	22	123	122	114	114	114
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	874	12648	12333	13122	13122	13122
1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7392	36056	33426	156056	156056	156056
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	18	171	171	111	111	111
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	24	133	133	123	123	123
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	930	12970	12664	13865	13865	13865
1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7476	36028	33379	155012	155012	155012
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	172	413	413	222	222	222
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	410	574	573	332	332	332
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	1721	21120	20278	32305	32305	32305
FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7044	37113	34314	189936	189936	189936
NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconflicted_germline_custom.ann_snpEff_VEP.ann	1045	17482	16880	31237	31237	31237
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	47	192	192	124	124	124
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	4	121	120	120	120	121
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	847	11891	11616	12422	12422	12422
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7724	36320	33635	161696	161696	161696
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	40	179	179	124	124	124
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	4	112	111	118	118	119
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	913	12436	12134	13192	13192	13192
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7764	36360	33658	164035	164035	164035
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	26	171	171	113	113	113
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	5	112	111	123	123	124
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	934	12647	12335	13340	13340	13340
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7836	36467	33741	164633	164633	164633
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	14	142	142	96	96	96
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	22	128	127	112	112	113
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	896	12671	12351	13203	13203	13203
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7786	36376	33700	163023	163023	163023
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	62	197	196	125	125	125
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	30	105	105	102	102	102
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	802	11557	11296	11915	11915	11915
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7608	36390	33653	159051	159051	159051
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	59	195	195	129	129	129
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	30	86	86	96	96	96
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	894	12109	11829	12647	12647	12647
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7646	36405	33685	161306	161306	161306
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	44	178	178	111	111	111
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	30	92	92	91	91	91
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	892	12363	12097	12856	12856	12856
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7704	36473	33724	161780	161780	161780
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.diploid_sv_custom.ann_snpEff_VEP.ann	14	135	135	98	98	98
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann	46	101	101	83	83	83
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels_custom.ann_snpEff_VEP.ann	856	12300	12011	12650	12650	12650
PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann	7708	36438	33720	160264	160264	160264

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: vep-general-stats_table

Sort	Column	Description	ID	Scale
\|\|	Overlapped regulatory features	Overlapped regulatory features	`vep-Overlapped_regulatory_features`
\|\|	Overlapped transcripts	Overlapped transcripts	`vep-Overlapped_transcripts`
\|\|	Overlapped genes	Overlapped genes	`vep-Overlapped_genes`
\|\|	Existing variants	Existing variants	`vep-Existing_variants`	variants
\|\|	Novel variants	Novel variants	`vep-Novel_variants`	variants
\|\|	Variants filtered out	Variants filtered out	`vep-Variants_filtered_out`	variants
\|\|	Variants processed	Variants processed	`vep-Variants_processed`	variants
\|\|	Lines of input read	Lines of input read	`vep-Lines_of_input_read`

Variant classes

Classes of variants found in the data.

Created with MultiQC

Consequences

Predicted consequences of variations.

Created with MultiQC

SIFT summary

SIFT variant effect prediction.

Created with MultiQC

PolyPhen summary

PolyPhen variant effect prediction.

Created with MultiQC

Variants by chromosome

Number of variants found on each chromosome.

Created with MultiQC

Position in protein

Relative position of affected amino acids in protein.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Group	Software	Version
AGGREGATE_VARIANT_QC	aggregate_qc_metrics	`2.0.0`
	python	`3.12.6`
ANNOTATE_BED_INFO	bcftools	`1.22`
BCFTOOLS_ANNOTATE	bcftools	`1.2`
BCFTOOLS_CONCAT	bcftools	`1.2`
BCFTOOLS_MPILEUP	bcftools	`1.2`
BCFTOOLS_QUERY	bcftools	`1.22`
BCFTOOLS_STATS	bcftools	`1.2`
CNVKIT_BATCH	cnvkit	`0.9.10`
	samtools	`1.17`
CNVKIT_CALL	cnvkit	`0.9.10`
CNVKIT_EXPORT	cnvkit	`0.9.10`
CNVKIT_GENEMETRICS	cnvkit	`0.9.10`
CNV_FACETS	facets	`0.6.2`
CONCAT_WHATSHAP_TNSEQ_VCFS	bcftools	`1.2`
CONCAT_WHATSHAP_VCFS	bcftools	`1.2`
CONPAIR_CONTAMINATION	conpair	`1.0`
	numpy	`1.24.4`
	python	`3.8.20`
CONPAIR_PILEUP	conpair	`1.0`
	gatk	`4.6.2.0 Using`
	python	`3.8.20`
CRAM_FILTER_HLA	sambamba	`null`
	samtools	`1.23`
DIFF_DV_SENTIEON	cyvcf2	`0.31.1`
	python	`3.11.14`
DV_RESCUE	deepvariant	`1.6.1`
ENSEMBLVEP_VEP	ensemblvep	`113.0`
EXTRACT_CHROMOSOMES	bcftools	`1.22`
EXTRACT_CHROMOSOMES_TNSEQ	bcftools	`1.22`
GT_CORRECTION	bedtools	`2.31.1`
	cyvcf2	`0.31.1`
	lightgbm	`4.6.0`
	python	`3.11.14`
HARD_FILTER_VCF	python	`3.9.15`
HLA_CONVERT_OPTITYPE	hla_to_json_vcf	`1.0.0`
	python	`3.13.11`
INDEL_ENTROPY_ANNOTATION	numpy	`2.4.0`
	pysam	`0.23.3`
	python	`3.13.11`
	scipy	`1.16.3`
LABEL_HOTSPOTS	python	`3.9.15`
MANTA_SOMATIC	manta	`1.6.0`
MERGE_FORCECALLED	bcftools	`1.22`
MERGE_SENTIEON_HAPLOTYPER_VCFS	gatk4	`4.5.0.0`
MERGE_STRELKA_INDELS	gatk4	`4.5.0.0`
MERGE_STRELKA_SNVS	gatk4	`4.5.0.0`
MIMSI_ANALYZE	mimsi	`0.4.5.1`
MSISENSOR2_MSI	msisensor2	`0.1`
Mosdepth	mosdepth	`0.3.8`
N7_COSMIC_SIGS	n7_cosmic_sigs	`0.0.1`
	r-base	`4.3.3`
OPTITYPE	optitype	`1.3.1`
PREP_STRELKA_INDEL	bcftools	`1.22`
PREP_TNSEQ_SNV	bcftools	`1.22`
SAMTOOLS_IDXSTATS_COUNT	bai_mapped_count	`1.0.0`
	python	`3.12.6`
SAMTOOLS_MPILEUP	samtools	`1.21`
SAMTOOLS_STATS	samtools	`1.21`
SCARHRD	scarHRD	`0.6.2`
SENTIEON_FORCECALL	sentieon	`202308.03`
SENTIEON_HAPLOTYPER	sentieon	`202308.03`
SENTIEON_HAPLOTYPER_RF_FILTER	bedtools	`2.31.1`
	cyvcf2	`0.31.1`
	lightgbm	`4.6.0`
	python	`3.11.14`
SENTIEON_TNFILTER	sentieon	`202308.03`
SENTIEON_TNHAPLOTYPER2	sentieon	`202308.03`
SEQTK_SAMPLE	seqtk	`1.4`
SNPEFF_SNPEFF	snpeff	`5.1d`
SPLIT_MULTIALLELIC	bcftools	`1.22`
STRELKA_SOMATIC	strelka	`2.9.10`
TABIX_BGZIPTABIX	tabix	`1.2`
TABIX_TABIX	tabix	`1.2`
TABIX_VEP	tabix	`1.2`
TIH_HRD_CALLING	hrd_calling	`0.0.1`
	r-base	`4.3.3`
TMB_SNV_INDEL	python	`3.9.15`
VARIANT_QC_TO_CSV	python	`3.12.6`
	variant_qc_to_csv	`1.0.0`
VCFTOOLS_TSTV_COUNT	vcftools	`0.1.16`
WHATSHAP	whatshap	`2.8`
WHATSHAP_TNSEQ	whatshap	`2.8`
Workflow	Nextflow	`25.10.2`
	altera/sarek	`v3.5.0-g44c19e3`

nf-core/sarek Methods Description

Suggested text and references to use when describing pipeline usage within the methods section of a publication.https://github.com/nf-core/sarek

Methods

Data was processed using nf-core/sarek v3.5.0 of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v25.10.2 (Di Tommaso et al., 2017) with the following command:

nextflow run 'https://gitlab.natera.com/rd-platform/bioinformatics/nextflow/sarek.git' 'https://gitlab.natera.com/rd-platform/bioinformatics/nextflow/sarek.git' -name sarek-cgp-dna-exp0035-tools-20260605-213512 -r 44c19e3df8f656f58cb9ee7cf60c60a25f789383 -profile eks,docker,std_run --input 's3://natera-platform-sandbox/platform-users/sgreer/samplesheets/samplesheet_sarek_cgp_dna_exp0035.csv' --outdir 's3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0035/tools__44c19e3d--20260605-213512' -output-dir 's3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0035/tools__44c19e3d--20260605-213512'

References

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192

Notes:

If available, make sure to update the text to include the Zenodo DOI of the pipeline version used.
The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

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