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.
Report
generated on 2026-02-10, 04:25 UTC
based on data in:
/tmp/nxf.S6C2cACLxO
General Statistics
Showing 704 samples.
Created with MultiQC
Bcftools
Utilities for variant calling and manipulating VCFs and BCFs.URL: https://samtools.github.io/bcftoolsDOI: 10.1093/gigascience/giab008
Variant Substitution Types
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.URL: 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).URL: 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.
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
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.
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.
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.URL: 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 0/352 rows and 7/8 columns.
| Sample Name | Overlapped regulatory features | Overlapped transcripts | Overlapped genes | Existing variants | Novel variants | Variants filtered out | Variants processed | Lines of input read |
|---|---|---|---|---|---|---|---|---|
| 1029_032-N1-BDNA-1_2375WFLT3_s01.entropy.entropy_custom.ann_snpEff_VEP.ann | 999 | 17321 | 16720 | 29444 | 0 | 0 | 29444 | 29444 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 42 | 172 | 172 | 127 | 0 | 0 | 127 | 127 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 5 | 79 | 79 | 125 | 0 | 0 | 125 | 125 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.mutect2.filtered_custom.ann_snpEff_VEP.ann | 260 | 4656 | 4596 | 8100 | 0 | 0 | 8100 | 8100 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 260 | 4656 | 4596 | 8100 | 0 | 0 | 8100 | 8100 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 164 | 2837 | 2814 | 2113 | 0 | 0 | 2113 | 2113 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 473 | 12502 | 12159 | 17234 | 0 | 0 | 17234 | 17234 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.tnseq.filtered_custom.ann_snpEff_VEP.ann | 910 | 17354 | 16783 | 31153 | 0 | 0 | 31153 | 31153 |
| 1029_05O-N1-BDNA-1_2375WFLT3_s02.entropy.entropy_custom.ann_snpEff_VEP.ann | 954 | 17300 | 16692 | 28635 | 0 | 0 | 28635 | 28635 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 42 | 179 | 179 | 139 | 0 | 0 | 139 | 140 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 12 | 12 | 16 | 0 | 0 | 16 | 16 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.mutect2.filtered_custom.ann_snpEff_VEP.ann | 224 | 4226 | 4175 | 5798 | 0 | 0 | 5798 | 5798 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 224 | 4226 | 4175 | 5798 | 0 | 0 | 5798 | 5798 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 143 | 2399 | 2381 | 1701 | 0 | 0 | 1701 | 1701 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 621 | 12702 | 12344 | 17182 | 0 | 0 | 17182 | 17182 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.tnseq.filtered_custom.ann_snpEff_VEP.ann | 847 | 17046 | 16483 | 27638 | 0 | 0 | 27638 | 27638 |
| 1029_0DT-N1-BDNA-1_2375WFLT3_s03.entropy.entropy_custom.ann_snpEff_VEP.ann | 1009 | 17460 | 16838 | 29791 | 0 | 0 | 29791 | 29791 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 50 | 195 | 195 | 142 | 0 | 0 | 142 | 142 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 17 | 59 | 59 | 83 | 0 | 0 | 83 | 84 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.mutect2.filtered_custom.ann_snpEff_VEP.ann | 274 | 4625 | 4575 | 8439 | 0 | 0 | 8439 | 8439 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 274 | 4625 | 4575 | 8439 | 0 | 0 | 8439 | 8439 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 156 | 2928 | 2907 | 2072 | 0 | 0 | 2072 | 2072 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 417 | 9032 | 8864 | 10687 | 0 | 0 | 10687 | 10687 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.tnseq.filtered_custom.ann_snpEff_VEP.ann | 932 | 17476 | 16899 | 30959 | 0 | 0 | 30959 | 30959 |
| 1029_0NX-N1-BDNA-1_2375WFLT3_s04.entropy.entropy_custom.ann_snpEff_VEP.ann | 1035 | 17990 | 17349 | 31193 | 0 | 0 | 31193 | 31193 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 71 | 190 | 190 | 140 | 0 | 0 | 140 | 140 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 3 | 105 | 105 | 160 | 0 | 0 | 160 | 162 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.mutect2.filtered_custom.ann_snpEff_VEP.ann | 313 | 5295 | 5238 | 9297 | 0 | 0 | 9297 | 9297 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 313 | 5295 | 5238 | 9297 | 0 | 0 | 9297 | 9297 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 155 | 2897 | 2875 | 2010 | 0 | 0 | 2010 | 2010 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 402 | 10045 | 9846 | 12531 | 0 | 0 | 12531 | 12531 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.tnseq.filtered_custom.ann_snpEff_VEP.ann | 993 | 18275 | 17670 | 33353 | 0 | 0 | 33353 | 33353 |
| 1029_1G0-N1-BDNA-1_2375WFLT3_s05.entropy.entropy_custom.ann_snpEff_VEP.ann | 1022 | 17467 | 16845 | 30819 | 0 | 0 | 30819 | 30819 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 28 | 189 | 189 | 142 | 0 | 0 | 142 | 142 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 15 | 109 | 109 | 113 | 0 | 0 | 113 | 113 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.mutect2.filtered_custom.ann_snpEff_VEP.ann | 546 | 12011 | 11733 | 19509 | 0 | 0 | 19509 | 19509 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 546 | 12011 | 11733 | 19509 | 0 | 0 | 19509 | 19509 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 182 | 3407 | 3372 | 2541 | 0 | 0 | 2541 | 2541 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 942 | 18268 | 17617 | 29758 | 0 | 0 | 29758 | 29758 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1166 | 20916 | 20102 | 43450 | 0 | 0 | 43450 | 43450 |
| 1029_1H5-N1-BDNA-1_2375WFLT3_s06.entropy.entropy_custom.ann_snpEff_VEP.ann | 29 | 173 | 173 | 114 | 0 | 0 | 114 | 114 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 10 | 168 | 168 | 134 | 0 | 0 | 134 | 134 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 42 | 42 | 73 | 0 | 0 | 73 | 73 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.mutect2.filtered_custom.ann_snpEff_VEP.ann | 289 | 4741 | 4675 | 7790 | 0 | 0 | 7790 | 7790 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 289 | 4741 | 4675 | 7790 | 0 | 0 | 7790 | 7790 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 151 | 2969 | 2941 | 2233 | 0 | 0 | 2233 | 2233 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 554 | 13074 | 12712 | 17850 | 0 | 0 | 17850 | 17850 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.tnseq.filtered_custom.ann_snpEff_VEP.ann | 931 | 17613 | 17000 | 31044 | 0 | 0 | 31044 | 31044 |
| 1029_2IN-N1-BDNA-1_2375WFLT3_s07.entropy.entropy_custom.ann_snpEff_VEP.ann | 1007 | 17291 | 16709 | 29363 | 0 | 0 | 29363 | 29363 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 68 | 204 | 204 | 133 | 0 | 0 | 133 | 133 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 16 | 112 | 112 | 175 | 0 | 0 | 175 | 177 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.mutect2.filtered_custom.ann_snpEff_VEP.ann | 338 | 6776 | 6681 | 11724 | 0 | 0 | 11724 | 11724 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 338 | 6776 | 6681 | 11724 | 0 | 0 | 11724 | 11724 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 176 | 3317 | 3295 | 2481 | 0 | 0 | 2481 | 2481 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 550 | 12589 | 12290 | 16623 | 0 | 0 | 16623 | 16623 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.tnseq.filtered_custom.ann_snpEff_VEP.ann | 970 | 18242 | 17640 | 35268 | 0 | 0 | 35268 | 35268 |
| 1029_2LI-N1-BDNA-1_2375WFLT3_s08.entropy.entropy_custom.ann_snpEff_VEP.ann | 1002 | 17409 | 16777 | 30800 | 0 | 0 | 30800 | 30800 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 50 | 208 | 208 | 149 | 0 | 0 | 149 | 149 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 46 | 45 | 58 | 0 | 0 | 58 | 60 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.filtered_custom.ann_snpEff_VEP.ann | 275 | 5330 | 5269 | 8115 | 0 | 0 | 8115 | 8115 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 275 | 5330 | 5269 | 8115 | 0 | 0 | 8115 | 8115 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 121 | 2671 | 2653 | 1944 | 0 | 0 | 1944 | 1944 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 285 | 8321 | 8177 | 9412 | 0 | 0 | 9412 | 9412 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.tnseq.filtered_custom.ann_snpEff_VEP.ann | 890 | 17640 | 17061 | 31243 | 0 | 0 | 31243 | 31243 |
| 1029_3N0-N1-BDNA-1_2375WFLT3_s09.entropy.entropy_custom.ann_snpEff_VEP.ann | 56 | 154 | 154 | 116 | 0 | 0 | 116 | 116 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 55 | 154 | 154 | 128 | 0 | 0 | 128 | 128 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 4 | 55 | 55 | 82 | 0 | 0 | 82 | 82 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.mutect2.filtered_custom.ann_snpEff_VEP.ann | 290 | 5609 | 5534 | 10209 | 0 | 0 | 10209 | 10209 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 290 | 5609 | 5534 | 10209 | 0 | 0 | 10209 | 10209 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 165 | 2911 | 2887 | 2120 | 0 | 0 | 2120 | 2120 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 351 | 9543 | 9355 | 11317 | 0 | 0 | 11317 | 11317 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.tnseq.filtered_custom.ann_snpEff_VEP.ann | 908 | 17587 | 17002 | 33440 | 0 | 0 | 33440 | 33440 |
| 1029_3OH-N1-BDNA-1_2375WFLT3_s10.entropy.entropy_custom.ann_snpEff_VEP.ann | 1001 | 17295 | 16698 | 30356 | 0 | 0 | 30356 | 30356 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 42 | 186 | 186 | 134 | 0 | 0 | 134 | 134 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 16 | 28 | 28 | 28 | 0 | 0 | 28 | 28 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.mutect2.filtered_custom.ann_snpEff_VEP.ann | 286 | 4560 | 4504 | 8505 | 0 | 0 | 8505 | 8505 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 286 | 4560 | 4504 | 8505 | 0 | 0 | 8505 | 8505 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 150 | 2920 | 2893 | 2074 | 0 | 0 | 2074 | 2074 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 292 | 8453 | 8319 | 9804 | 0 | 0 | 9804 | 9804 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.tnseq.filtered_custom.ann_snpEff_VEP.ann | 928 | 17213 | 16658 | 31402 | 0 | 0 | 31402 | 31402 |
| 1029_4J3-N1-BDNA-1_2375WFLT3_s11.entropy.entropy_custom.ann_snpEff_VEP.ann | 1010 | 17533 | 16914 | 30438 | 0 | 0 | 30438 | 30438 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 28 | 165 | 165 | 115 | 0 | 0 | 115 | 116 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 53 | 53 | 77 | 0 | 0 | 77 | 77 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.mutect2.filtered_custom.ann_snpEff_VEP.ann | 278 | 4686 | 4629 | 7638 | 0 | 0 | 7638 | 7638 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 278 | 4686 | 4629 | 7638 | 0 | 0 | 7638 | 7638 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 116 | 2660 | 2644 | 1880 | 0 | 0 | 1880 | 1880 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 356 | 8532 | 8363 | 10928 | 0 | 0 | 10928 | 10928 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.tnseq.filtered_custom.ann_snpEff_VEP.ann | 910 | 17470 | 16910 | 30468 | 0 | 0 | 30468 | 30468 |
| 1029_4Z2-N1-BDNA-1_2375WFLT3_s12.entropy.entropy_custom.ann_snpEff_VEP.ann | 1009 | 17328 | 16726 | 30034 | 0 | 0 | 30034 | 30034 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 32 | 158 | 157 | 107 | 0 | 0 | 107 | 107 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 78 | 78 | 110 | 0 | 0 | 110 | 110 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.mutect2.filtered_custom.ann_snpEff_VEP.ann | 515 | 11214 | 10969 | 17602 | 0 | 0 | 17602 | 17602 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 515 | 11214 | 10969 | 17602 | 0 | 0 | 17602 | 17602 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 189 | 3364 | 3334 | 2479 | 0 | 0 | 2479 | 2479 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 826 | 16801 | 16250 | 25045 | 0 | 0 | 25045 | 25045 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1130 | 20428 | 19653 | 40888 | 0 | 0 | 40888 | 40888 |
| 1029_56D-N1-BDNA-1_2375WFLT3_s13.entropy.entropy_custom.ann_snpEff_VEP.ann | 30 | 136 | 136 | 99 | 0 | 0 | 99 | 99 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 30 | 162 | 162 | 112 | 0 | 0 | 112 | 112 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 6 | 73 | 73 | 80 | 0 | 0 | 80 | 81 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.mutect2.filtered_custom.ann_snpEff_VEP.ann | 330 | 7394 | 7284 | 11118 | 0 | 0 | 11118 | 11118 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 330 | 7394 | 7284 | 11118 | 0 | 0 | 11118 | 11118 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 144 | 2912 | 2888 | 2096 | 0 | 0 | 2096 | 2096 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 444 | 11878 | 11618 | 16045 | 0 | 0 | 16045 | 16045 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.tnseq.filtered_custom.ann_snpEff_VEP.ann | 934 | 18532 | 17903 | 33710 | 0 | 0 | 33710 | 33710 |
| 1029_5IX-N1-BDNA-1_2375WFLT3_s14.entropy.entropy_custom.ann_snpEff_VEP.ann | 1122 | 18711 | 18020 | 33068 | 0 | 0 | 33068 | 33068 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 63 | 175 | 175 | 124 | 0 | 0 | 124 | 124 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 16 | 16 | 32 | 0 | 0 | 32 | 32 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.mutect2.filtered_custom.ann_snpEff_VEP.ann | 260 | 5178 | 5119 | 7888 | 0 | 0 | 7888 | 7888 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 260 | 5178 | 5119 | 7888 | 0 | 0 | 7888 | 7888 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 129 | 2733 | 2714 | 2053 | 0 | 0 | 2053 | 2053 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 405 | 10103 | 9884 | 11648 | 0 | 0 | 11648 | 11648 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1023 | 18849 | 18191 | 33784 | 0 | 0 | 33784 | 33784 |
| 1029_5O3-N1-BDNA-1_2375WFLT3_s15.entropy.entropy_custom.ann_snpEff_VEP.ann | 1003 | 17438 | 16825 | 30243 | 0 | 0 | 30243 | 30243 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 48 | 183 | 183 | 122 | 0 | 0 | 122 | 123 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 20 | 70 | 70 | 84 | 0 | 0 | 84 | 84 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.mutect2.filtered_custom.ann_snpEff_VEP.ann | 705 | 14532 | 14138 | 22418 | 0 | 0 | 22418 | 22418 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 705 | 14532 | 14138 | 22418 | 0 | 0 | 22418 | 22418 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 219 | 3745 | 3712 | 2841 | 0 | 0 | 2841 | 2841 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1248 | 21169 | 20321 | 38490 | 0 | 0 | 38490 | 38490 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1288 | 22249 | 21337 | 45428 | 0 | 0 | 45428 | 45428 |
| 1029_7Y1-N1-BDNA-1_2375WFLT3_s16.entropy.entropy_custom.ann_snpEff_VEP.ann | 1011 | 17429 | 16818 | 29970 | 0 | 0 | 29970 | 29970 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 33 | 152 | 152 | 118 | 0 | 0 | 118 | 119 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 81 | 81 | 103 | 0 | 0 | 103 | 103 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.mutect2.filtered_custom.ann_snpEff_VEP.ann | 389 | 8892 | 8737 | 16614 | 0 | 0 | 16614 | 16614 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 389 | 8892 | 8737 | 16614 | 0 | 0 | 16614 | 16614 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 148 | 2948 | 2920 | 2198 | 0 | 0 | 2198 | 2198 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 695 | 15755 | 15286 | 21964 | 0 | 0 | 21964 | 21964 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1044 | 19343 | 18672 | 41051 | 0 | 0 | 41051 | 41051 |
| 1029_8AV-N1-BDNA-1_2375WFLT3_s17.entropy.entropy_custom.ann_snpEff_VEP.ann | 1027 | 17657 | 17033 | 30042 | 0 | 0 | 30042 | 30042 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 39 | 151 | 151 | 122 | 0 | 0 | 122 | 123 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 72 | 72 | 92 | 0 | 0 | 92 | 92 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.mutect2.filtered_custom.ann_snpEff_VEP.ann | 285 | 4965 | 4900 | 8557 | 0 | 0 | 8557 | 8557 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 285 | 4965 | 4900 | 8557 | 0 | 0 | 8557 | 8557 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 154 | 2771 | 2740 | 2019 | 0 | 0 | 2019 | 2019 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 507 | 11458 | 11178 | 16406 | 0 | 0 | 16406 | 16406 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.tnseq.filtered_custom.ann_snpEff_VEP.ann | 936 | 17695 | 17117 | 31441 | 0 | 0 | 31441 | 31441 |
| 1029_8BO-N1-BDNA-1_2375WFLT3_s18.entropy.entropy_custom.ann_snpEff_VEP.ann | 978 | 17406 | 16814 | 29609 | 0 | 0 | 29609 | 29609 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 34 | 177 | 177 | 125 | 0 | 0 | 125 | 125 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 52 | 52 | 73 | 0 | 0 | 73 | 73 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.mutect2.filtered_custom.ann_snpEff_VEP.ann | 315 | 6352 | 6257 | 11925 | 0 | 0 | 11925 | 11925 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 315 | 6352 | 6257 | 11925 | 0 | 0 | 11925 | 11925 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 135 | 2658 | 2642 | 1883 | 0 | 0 | 1883 | 1883 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 317 | 8825 | 8648 | 10203 | 0 | 0 | 10203 | 10203 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.tnseq.filtered_custom.ann_snpEff_VEP.ann | 945 | 18110 | 17505 | 35881 | 0 | 0 | 35881 | 35881 |
| 1029_8OI-N1-BDNA-1_2375WFLT3_s19.entropy.entropy_custom.ann_snpEff_VEP.ann | 1014 | 17335 | 16730 | 30725 | 0 | 0 | 30725 | 30725 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 39 | 189 | 189 | 147 | 0 | 0 | 147 | 147 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 5 | 91 | 91 | 128 | 0 | 0 | 128 | 129 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.mutect2.filtered_custom.ann_snpEff_VEP.ann | 415 | 7717 | 7611 | 13881 | 0 | 0 | 13881 | 13881 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 415 | 7717 | 7611 | 13881 | 0 | 0 | 13881 | 13881 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 191 | 3247 | 3221 | 2464 | 0 | 0 | 2464 | 2464 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 653 | 14558 | 14146 | 20415 | 0 | 0 | 20415 | 20415 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1052 | 18706 | 18064 | 37982 | 0 | 0 | 37982 | 37982 |
| 1029_BA0-N2-BDNA-1_2375WFLT3_s20.entropy.entropy_custom.ann_snpEff_VEP.ann | 1006 | 17858 | 17222 | 29902 | 0 | 0 | 29902 | 29902 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 25 | 191 | 191 | 139 | 0 | 0 | 139 | 140 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 19 | 53 | 53 | 47 | 0 | 0 | 47 | 47 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.mutect2.filtered_custom.ann_snpEff_VEP.ann | 228 | 4055 | 4012 | 6471 | 0 | 0 | 6471 | 6471 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 228 | 4055 | 4012 | 6471 | 0 | 0 | 6471 | 6471 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 126 | 2824 | 2804 | 2098 | 0 | 0 | 2098 | 2098 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 423 | 9584 | 9371 | 12731 | 0 | 0 | 12731 | 12731 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.tnseq.filtered_custom.ann_snpEff_VEP.ann | 884 | 17603 | 17023 | 29816 | 0 | 0 | 29816 | 29816 |
| 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.entropy.entropy_custom.ann_snpEff_VEP.ann | 999 | 17387 | 16772 | 30552 | 0 | 0 | 30552 | 30552 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 32 | 143 | 143 | 110 | 0 | 0 | 110 | 110 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 37 | 37 | 42 | 0 | 0 | 42 | 42 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.filtered_custom.ann_snpEff_VEP.ann | 157 | 5174 | 5134 | 4411 | 0 | 0 | 4411 | 4411 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 157 | 5174 | 5134 | 4411 | 0 | 0 | 4411 | 4411 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 67 | 1526 | 1508 | 1511 | 0 | 0 | 1511 | 1511 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 668 | 17772 | 17165 | 26985 | 0 | 0 | 26985 | 26985 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tnseq.filtered_custom.ann_snpEff_VEP.ann | 770 | 17138 | 16577 | 25281 | 0 | 0 | 25281 | 25281 |
| 1029_BBOC-N1-BDNA-1_2375WFLT3_s22.entropy.entropy_custom.ann_snpEff_VEP.ann | 1011 | 17474 | 16876 | 31077 | 0 | 0 | 31077 | 31077 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 27 | 163 | 163 | 123 | 0 | 0 | 123 | 123 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 69 | 69 | 67 | 0 | 0 | 67 | 68 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.mutect2.filtered_custom.ann_snpEff_VEP.ann | 258 | 4777 | 4718 | 8369 | 0 | 0 | 8369 | 8369 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 258 | 4777 | 4718 | 8369 | 0 | 0 | 8369 | 8369 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 135 | 2893 | 2864 | 2082 | 0 | 0 | 2082 | 2082 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 551 | 12012 | 11695 | 17436 | 0 | 0 | 17436 | 17436 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.tnseq.filtered_custom.ann_snpEff_VEP.ann | 901 | 17468 | 16912 | 31690 | 0 | 0 | 31690 | 31690 |
| 1029_BBS1-N1-BDNA-1_2375WFLT3_s23.entropy.entropy_custom.ann_snpEff_VEP.ann | 980 | 17485 | 16860 | 29255 | 0 | 0 | 29255 | 29255 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 15 | 148 | 148 | 119 | 0 | 0 | 119 | 120 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 63 | 63 | 78 | 0 | 0 | 78 | 78 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.filtered_custom.ann_snpEff_VEP.ann | 313 | 5091 | 5026 | 9192 | 0 | 0 | 9192 | 9192 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 313 | 5091 | 5026 | 9192 | 0 | 0 | 9192 | 9192 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 161 | 3064 | 3033 | 2258 | 0 | 0 | 2258 | 2258 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 413 | 10157 | 9932 | 12962 | 0 | 0 | 12962 | 12962 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.tnseq.filtered_custom.ann_snpEff_VEP.ann | 959 | 17784 | 17175 | 32264 | 0 | 0 | 32264 | 32264 |
| 1029_BCB6-N1-BDNA-1_2375WFLT3_s24.entropy.entropy_custom.ann_snpEff_VEP.ann | 47 | 168 | 168 | 114 | 0 | 0 | 114 | 114 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 41 | 150 | 150 | 112 | 0 | 0 | 112 | 112 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 6 | 109 | 108 | 136 | 0 | 0 | 136 | 136 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.mutect2.filtered_custom.ann_snpEff_VEP.ann | 418 | 8971 | 8786 | 19620 | 0 | 0 | 19620 | 19620 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 418 | 8971 | 8786 | 19620 | 0 | 0 | 19620 | 19620 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 195 | 3187 | 3152 | 2391 | 0 | 0 | 2391 | 2391 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 554 | 12869 | 12533 | 17075 | 0 | 0 | 17075 | 17075 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1055 | 19158 | 18457 | 43551 | 0 | 0 | 43551 | 43551 |
| 1029_BCTO-N1-BDNA-1_2375WFLT3_s25.entropy.entropy_custom.ann_snpEff_VEP.ann | 29 | 155 | 155 | 100 | 0 | 0 | 100 | 100 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 26 | 171 | 171 | 103 | 0 | 0 | 103 | 104 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 62 | 146 | 146 | 90 | 0 | 0 | 90 | 90 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.mutect2.filtered_custom.ann_snpEff_VEP.ann | 745 | 15095 | 14670 | 24733 | 0 | 0 | 24733 | 24733 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 745 | 15095 | 14670 | 24733 | 0 | 0 | 24733 | 24733 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 266 | 3947 | 3896 | 3337 | 0 | 0 | 3337 | 3337 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1306 | 22342 | 21441 | 42348 | 0 | 0 | 42348 | 42348 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1339 | 22561 | 21624 | 47874 | 0 | 0 | 47874 | 47874 |
| 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.entropy.entropy_custom.ann_snpEff_VEP.ann | 29 | 157 | 157 | 113 | 0 | 0 | 113 | 113 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 28 | 181 | 181 | 137 | 0 | 0 | 137 | 138 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 12 | 12 | 15 | 0 | 0 | 15 | 16 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.mutect2.filtered_custom.ann_snpEff_VEP.ann | 216 | 3756 | 3714 | 5781 | 0 | 0 | 5781 | 5781 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 216 | 3756 | 3714 | 5781 | 0 | 0 | 5781 | 5781 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 157 | 2955 | 2930 | 2160 | 0 | 0 | 2160 | 2160 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 546 | 12412 | 12065 | 16624 | 0 | 0 | 16624 | 16624 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.tnseq.filtered_custom.ann_snpEff_VEP.ann | 881 | 17408 | 16819 | 29357 | 0 | 0 | 29357 | 29357 |
| 1029_BF2U-N1-BDNA-1_2375WFLT3_s27.entropy.entropy_custom.ann_snpEff_VEP.ann | 998 | 17100 | 16510 | 28701 | 0 | 0 | 28701 | 28701 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 22 | 144 | 144 | 102 | 0 | 0 | 102 | 102 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 3 | 23 | 23 | 32 | 0 | 0 | 32 | 32 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.mutect2.filtered_custom.ann_snpEff_VEP.ann | 239 | 4108 | 4069 | 5883 | 0 | 0 | 5883 | 5883 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 239 | 4108 | 4069 | 5883 | 0 | 0 | 5883 | 5883 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 120 | 2540 | 2525 | 1780 | 0 | 0 | 1780 | 1780 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 221 | 6393 | 6307 | 6261 | 0 | 0 | 6261 | 6261 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.tnseq.filtered_custom.ann_snpEff_VEP.ann | 865 | 16770 | 16247 | 27803 | 0 | 0 | 27803 | 27803 |
| 1029_BFKM-N1-BDNA-1_2375WFLT3_s28.entropy.entropy_custom.ann_snpEff_VEP.ann | 992 | 17309 | 16700 | 29897 | 0 | 0 | 29897 | 29897 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 33 | 150 | 150 | 131 | 0 | 0 | 131 | 132 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 18 | 114 | 114 | 123 | 0 | 0 | 123 | 124 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.mutect2.filtered_custom.ann_snpEff_VEP.ann | 435 | 9499 | 9323 | 17744 | 0 | 0 | 17744 | 17744 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 435 | 9499 | 9323 | 17744 | 0 | 0 | 17744 | 17744 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 184 | 3239 | 3209 | 2450 | 0 | 0 | 2450 | 2450 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 600 | 14095 | 13723 | 19627 | 0 | 0 | 19627 | 19627 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1043 | 19454 | 18773 | 41329 | 0 | 0 | 41329 | 41329 |
| 1029_BG5-N1-BDNA-1_2375WFLT3_s29.entropy.entropy_custom.ann_snpEff_VEP.ann | 1034 | 17632 | 17017 | 31082 | 0 | 0 | 31082 | 31082 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 27 | 150 | 150 | 117 | 0 | 0 | 117 | 117 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 8 | 8 | 14 | 0 | 0 | 14 | 14 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.filtered_custom.ann_snpEff_VEP.ann | 29 | 1197 | 1193 | 1079 | 0 | 0 | 1079 | 1079 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 29 | 1197 | 1193 | 1079 | 0 | 0 | 1079 | 1079 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 185 | 2781 | 2757 | 2533 | 0 | 0 | 2533 | 2533 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 893 | 19561 | 18891 | 27603 | 0 | 0 | 27603 | 27603 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tnseq.filtered_custom.ann_snpEff_VEP.ann | 662 | 15375 | 14913 | 21855 | 0 | 0 | 21855 | 21855 |
| 1029_BGFD-N1-BDNA-1_2375WFLT3_s30.entropy.entropy_custom.ann_snpEff_VEP.ann | 965 | 17266 | 16661 | 29446 | 0 | 0 | 29446 | 29446 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 43 | 134 | 134 | 107 | 0 | 0 | 107 | 107 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 3 | 57 | 57 | 77 | 0 | 0 | 77 | 78 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.filtered_custom.ann_snpEff_VEP.ann | 323 | 6632 | 6536 | 12835 | 0 | 0 | 12835 | 12835 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 323 | 6632 | 6536 | 12835 | 0 | 0 | 12835 | 12835 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 168 | 3178 | 3156 | 2294 | 0 | 0 | 2294 | 2294 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 310 | 9959 | 9772 | 11340 | 0 | 0 | 11340 | 11340 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tnseq.filtered_custom.ann_snpEff_VEP.ann | 930 | 18057 | 17455 | 36423 | 0 | 0 | 36423 | 36423 |
| 1029_BGMF-N1-BDNA-1_2375WFLT3_s31.entropy.entropy_custom.ann_snpEff_VEP.ann | 1022 | 17416 | 16789 | 31010 | 0 | 0 | 31010 | 31010 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 33 | 183 | 183 | 138 | 0 | 0 | 138 | 139 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 24 | 65 | 65 | 65 | 0 | 0 | 65 | 66 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.mutect2.filtered_custom.ann_snpEff_VEP.ann | 245 | 4203 | 4150 | 6869 | 0 | 0 | 6869 | 6869 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 245 | 4203 | 4150 | 6869 | 0 | 0 | 6869 | 6869 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 135 | 2506 | 2484 | 1787 | 0 | 0 | 1787 | 1787 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 368 | 8296 | 8149 | 10464 | 0 | 0 | 10464 | 10464 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.tnseq.filtered_custom.ann_snpEff_VEP.ann | 890 | 17156 | 16591 | 30033 | 0 | 0 | 30033 | 30033 |
| 1029_BICA-N1-BDNA-1_2375WFLT3_s32.entropy.entropy_custom.ann_snpEff_VEP.ann | 1012 | 17235 | 16599 | 30484 | 0 | 0 | 30484 | 30484 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 22 | 189 | 189 | 169 | 0 | 0 | 169 | 169 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 10 | 84 | 84 | 102 | 0 | 0 | 102 | 102 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.filtered_custom.ann_snpEff_VEP.ann | 555 | 13405 | 13114 | 21738 | 0 | 0 | 21738 | 21738 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 555 | 13405 | 13114 | 21738 | 0 | 0 | 21738 | 21738 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 137 | 2760 | 2739 | 1992 | 0 | 0 | 1992 | 1992 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 540 | 15045 | 14691 | 22723 | 0 | 0 | 22723 | 22723 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1185 | 21377 | 20574 | 45153 | 0 | 0 | 45153 | 45153 |
| 1029_BIHC-N1-BDNA-1_2375WFLT3_s33.entropy.entropy_custom.ann_snpEff_VEP.ann | 1015 | 17382 | 16775 | 29981 | 0 | 0 | 29981 | 29981 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 46 | 169 | 169 | 144 | 0 | 0 | 144 | 144 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 19 | 50 | 50 | 65 | 0 | 0 | 65 | 66 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.mutect2.filtered_custom.ann_snpEff_VEP.ann | 279 | 4863 | 4805 | 7484 | 0 | 0 | 7484 | 7484 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 279 | 4863 | 4805 | 7484 | 0 | 0 | 7484 | 7484 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 153 | 2923 | 2904 | 2048 | 0 | 0 | 2048 | 2048 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 275 | 7726 | 7620 | 8440 | 0 | 0 | 8440 | 8440 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.tnseq.filtered_custom.ann_snpEff_VEP.ann | 917 | 17404 | 16841 | 29769 | 0 | 0 | 29769 | 29769 |
| 1029_BIHO-N1-BDNA-1_2375WFLT3_s34.entropy.entropy_custom.ann_snpEff_VEP.ann | 31 | 173 | 173 | 125 | 0 | 0 | 125 | 125 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 33 | 202 | 202 | 144 | 0 | 0 | 144 | 144 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 8 | 80 | 80 | 84 | 0 | 0 | 84 | 84 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.mutect2.filtered_custom.ann_snpEff_VEP.ann | 300 | 6026 | 5949 | 10013 | 0 | 0 | 10013 | 10013 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 300 | 6026 | 5949 | 10013 | 0 | 0 | 10013 | 10013 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 128 | 2543 | 2523 | 1832 | 0 | 0 | 1832 | 1832 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 357 | 9574 | 9391 | 13139 | 0 | 0 | 13139 | 13139 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.tnseq.filtered_custom.ann_snpEff_VEP.ann | 939 | 17787 | 17188 | 32878 | 0 | 0 | 32878 | 32878 |
| 1029_BJH0-N1-BDNA-1_2375WFLT3_s35.entropy.entropy_custom.ann_snpEff_VEP.ann | 38 | 156 | 156 | 100 | 0 | 0 | 100 | 101 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 24 | 131 | 131 | 102 | 0 | 0 | 102 | 102 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 48 | 48 | 69 | 0 | 0 | 69 | 69 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.mutect2.filtered_custom.ann_snpEff_VEP.ann | 376 | 7608 | 7489 | 13690 | 0 | 0 | 13690 | 13690 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 376 | 7608 | 7489 | 13690 | 0 | 0 | 13690 | 13690 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 169 | 3020 | 2995 | 2225 | 0 | 0 | 2225 | 2225 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 436 | 11130 | 10902 | 13835 | 0 | 0 | 13835 | 13835 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1033 | 18729 | 18067 | 37901 | 0 | 0 | 37901 | 37901 |
| 1029_BK2H-N1-BDNA-1_2375WFLT3_s36.entropy.entropy_custom.ann_snpEff_VEP.ann | 1010 | 17511 | 16881 | 29257 | 0 | 0 | 29257 | 29257 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 29 | 163 | 163 | 104 | 0 | 0 | 104 | 105 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 66 | 109 | 108 | 110 | 0 | 0 | 110 | 111 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.filtered_custom.ann_snpEff_VEP.ann | 636 | 13114 | 12787 | 20277 | 0 | 0 | 20277 | 20277 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 636 | 13114 | 12787 | 20277 | 0 | 0 | 20277 | 20277 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 215 | 3729 | 3691 | 2867 | 0 | 0 | 2867 | 2867 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1185 | 20569 | 19768 | 37528 | 0 | 0 | 37528 | 37528 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1227 | 21582 | 20721 | 43536 | 0 | 0 | 43536 | 43536 |
| 1029_BLH5-N1-BDNA-1_2375WFLT3_s37.entropy.entropy_custom.ann_snpEff_VEP.ann | 1039 | 17845 | 17177 | 31237 | 0 | 0 | 31237 | 31237 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 47 | 174 | 174 | 137 | 0 | 0 | 137 | 137 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 65 | 65 | 92 | 0 | 0 | 92 | 92 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.mutect2.filtered_custom.ann_snpEff_VEP.ann | 272 | 4703 | 4640 | 7651 | 0 | 0 | 7651 | 7651 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 272 | 4703 | 4640 | 7651 | 0 | 0 | 7651 | 7651 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 160 | 2957 | 2939 | 2130 | 0 | 0 | 2130 | 2130 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 532 | 11179 | 10927 | 14195 | 0 | 0 | 14195 | 14195 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.tnseq.filtered_custom.ann_snpEff_VEP.ann | 933 | 17733 | 17118 | 31109 | 0 | 0 | 31109 | 31109 |
| 1029_BLU1-N1-BDNA-1_2375WFLT3_s38.entropy.entropy_custom.ann_snpEff_VEP.ann | 977 | 17318 | 16709 | 29652 | 0 | 0 | 29652 | 29652 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 38 | 196 | 196 | 121 | 0 | 0 | 121 | 121 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 27 | 27 | 40 | 0 | 0 | 40 | 41 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.mutect2.filtered_custom.ann_snpEff_VEP.ann | 248 | 4132 | 4084 | 6806 | 0 | 0 | 6806 | 6806 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 248 | 4132 | 4084 | 6806 | 0 | 0 | 6806 | 6806 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 116 | 2510 | 2494 | 1743 | 0 | 0 | 1743 | 1743 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 203 | 6191 | 6114 | 7067 | 0 | 0 | 7067 | 7067 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.tnseq.filtered_custom.ann_snpEff_VEP.ann | 879 | 17045 | 16502 | 28895 | 0 | 0 | 28895 | 28895 |
| 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.entropy.entropy_custom.ann_snpEff_VEP.ann | 1008 | 17326 | 16725 | 29643 | 0 | 0 | 29643 | 29643 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 59 | 191 | 191 | 139 | 0 | 0 | 139 | 139 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 65 | 65 | 96 | 0 | 0 | 96 | 98 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.mutect2.filtered_custom.ann_snpEff_VEP.ann | 273 | 5532 | 5453 | 8935 | 0 | 0 | 8935 | 8935 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 273 | 5532 | 5453 | 8935 | 0 | 0 | 8935 | 8935 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 165 | 3171 | 3151 | 2372 | 0 | 0 | 2372 | 2372 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 603 | 12844 | 12484 | 17637 | 0 | 0 | 17637 | 17637 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.tnseq.filtered_custom.ann_snpEff_VEP.ann | 926 | 17738 | 17147 | 32173 | 0 | 0 | 32173 | 32173 |
| 1029_BNG8-N1-BDNA-1_2375WFLT3_s40.entropy.entropy_custom.ann_snpEff_VEP.ann | 997 | 17624 | 17000 | 30752 | 0 | 0 | 30752 | 30752 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 25 | 133 | 133 | 85 | 0 | 0 | 85 | 85 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 111 | 111 | 142 | 0 | 0 | 142 | 143 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.mutect2.filtered_custom.ann_snpEff_VEP.ann | 316 | 5610 | 5512 | 12921 | 0 | 0 | 12921 | 12921 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 316 | 5610 | 5512 | 12921 | 0 | 0 | 12921 | 12921 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 148 | 2891 | 2873 | 2127 | 0 | 0 | 2127 | 2127 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 222 | 7015 | 6895 | 8099 | 0 | 0 | 8099 | 8099 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.tnseq.filtered_custom.ann_snpEff_VEP.ann | 965 | 18127 | 17483 | 36714 | 0 | 0 | 36714 | 36714 |
| 1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.entropy.entropy_custom.ann_snpEff_VEP.ann | 977 | 17594 | 16994 | 30142 | 0 | 0 | 30142 | 30142 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 29 | 181 | 181 | 117 | 0 | 0 | 117 | 118 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 54 | 54 | 85 | 0 | 0 | 85 | 86 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.mutect2.filtered_custom.ann_snpEff_VEP.ann | 226 | 3764 | 3712 | 6815 | 0 | 0 | 6815 | 6815 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 226 | 3764 | 3712 | 6815 | 0 | 0 | 6815 | 6815 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 111 | 2250 | 2238 | 1584 | 0 | 0 | 1584 | 1584 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 280 | 7064 | 6958 | 8291 | 0 | 0 | 8291 | 8291 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.tnseq.filtered_custom.ann_snpEff_VEP.ann | 834 | 17113 | 16588 | 29301 | 0 | 0 | 29301 | 29301 |
| 1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.entropy.entropy_custom.ann_snpEff_VEP.ann | 53 | 145 | 145 | 116 | 0 | 0 | 116 | 116 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 54 | 161 | 161 | 134 | 0 | 0 | 134 | 134 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 31 | 89 | 89 | 94 | 0 | 0 | 94 | 94 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.mutect2.filtered_custom.ann_snpEff_VEP.ann | 670 | 14702 | 14319 | 22636 | 0 | 0 | 22636 | 22636 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 670 | 14702 | 14319 | 22636 | 0 | 0 | 22636 | 22636 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 206 | 3657 | 3619 | 2840 | 0 | 0 | 2840 | 2840 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1216 | 20757 | 19979 | 38812 | 0 | 0 | 38812 | 38812 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1243 | 22074 | 21202 | 45675 | 0 | 0 | 45675 | 45675 |
| 1029_BOSD-N1-BDNA-1_2375WFLT3_s43.entropy.entropy_custom.ann_snpEff_VEP.ann | 24 | 128 | 128 | 100 | 0 | 0 | 100 | 100 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 39 | 187 | 187 | 139 | 0 | 0 | 139 | 139 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 61 | 60 | 87 | 0 | 0 | 87 | 89 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.mutect2.filtered_custom.ann_snpEff_VEP.ann | 256 | 5669 | 5604 | 8430 | 0 | 0 | 8430 | 8430 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 256 | 5669 | 5604 | 8430 | 0 | 0 | 8430 | 8430 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 175 | 3186 | 3161 | 2297 | 0 | 0 | 2297 | 2297 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 440 | 10661 | 10421 | 13932 | 0 | 0 | 13932 | 13932 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.tnseq.filtered_custom.ann_snpEff_VEP.ann | 874 | 17649 | 17074 | 30760 | 0 | 0 | 30760 | 30760 |
| 1029_BP21-N1-BDNA-1_2375WFLT3_s44.entropy.entropy_custom.ann_snpEff_VEP.ann | 995 | 17485 | 16900 | 29479 | 0 | 0 | 29479 | 29479 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 45 | 148 | 148 | 151 | 0 | 0 | 151 | 152 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 44 | 44 | 61 | 0 | 0 | 61 | 62 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.mutect2.filtered_custom.ann_snpEff_VEP.ann | 202 | 3967 | 3925 | 6771 | 0 | 0 | 6771 | 6771 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 202 | 3967 | 3925 | 6771 | 0 | 0 | 6771 | 6771 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 113 | 2442 | 2429 | 1660 | 0 | 0 | 1660 | 1660 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 252 | 7539 | 7420 | 7818 | 0 | 0 | 7818 | 7818 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.tnseq.filtered_custom.ann_snpEff_VEP.ann | 840 | 17102 | 16559 | 29474 | 0 | 0 | 29474 | 29474 |
Variant classes
Classes of variants found in the data.
Consequences
Predicted consequences of variations.
SIFT summary
SIFT variant effect prediction.
PolyPhen summary
PolyPhen variant effect prediction.
Variants by chromosome
Number of variants found on each chromosome.
Position in protein
Relative position of affected amino acids in protein.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| AGGREGATE_VARIANT_QC | aggregate_qc_metrics | 1.0.0 |
| python | 3.12.6 | |
| ASCAT | alleleCounter | 4.3.0 |
| ascat | 3.1.1 | |
| BCFTOOLS_ANNOTATE | bcftools | 1.2 |
| BCFTOOLS_QUERY | bcftools | 1.22 |
| BCFTOOLS_STATS | bcftools | 1.2 |
| CALCULATECONTAMINATION | gatk4 | 4.5.0.0 |
| CNNSCOREVARIANTS | gatk4 | 4.5.0.0 |
| CNVKIT_BATCH | cnvkit | 0.9.10 |
| CNVKIT_CALL | cnvkit | 0.9.10 |
| CNVKIT_EXPORT | cnvkit | 0.9.10 |
| CNVKIT_GENEMETRICS | cnvkit | 0.9.10 |
| CNV_FACETS | facets | 0.6.2 |
| 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 | |
| ENSEMBLVEP_VEP | ensemblvep | 113.0 |
| FILTERMUTECTCALLS | gatk4 | 4.5.0.0 |
| FILTERVARIANTTRANCHES | gatk4 | 4.5.0.0 |
| GATHERPILEUPSUMMARIES_NORMAL | gatk4 | 4.5.0.0 |
| GATHERPILEUPSUMMARIES_TUMOR | gatk4 | 4.5.0.0 |
| GATK4_HAPLOTYPECALLER | gatk4 | 4.5.0.0 |
| GETPILEUPSUMMARIES_NORMAL | gatk4 | 4.5.0.0 |
| GETPILEUPSUMMARIES_TUMOR | gatk4 | 4.5.0.0 |
| 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 | |
| LEARNREADORIENTATIONMODEL | gatk4 | 4.5.0.0 |
| MANTA_GERMLINE | manta | 1.6.0 |
| MANTA_SOMATIC | manta | 1.6.0 |
| MERGEMUTECTSTATS | gatk4 | 4.5.0.0 |
| MERGE_HAPLOTYPECALLER | gatk4 | 4.5.0.0 |
| MERGE_MUTECT2 | gatk4 | 4.5.0.0 |
| MERGE_SENTIEON_HAPLOTYPER_VCFS | gatk4 | 4.5.0.0 |
| MERGE_STRELKA | gatk4 | 4.5.0.0 |
| MERGE_STRELKA_GENOME | gatk4 | 4.5.0.0 |
| MERGE_STRELKA_INDELS | gatk4 | 4.5.0.0 |
| MERGE_STRELKA_SNVS | gatk4 | 4.5.0.0 |
| MSISENSOR2_MSI | msisensor2 | 0.1 |
| MUTECT2_PAIRED | gatk4 | 4.5.0.0 |
| OPTITYPE | optitype | 1.3.1 |
| SAMTOOLS_MPILEUP | samtools | 1.21 |
| SCARHRD | scarHRD | 0.6.2 |
| SENTIEON_HAPLOTYPER | sentieon | 202308.03 |
| SENTIEON_TNFILTER | sentieon | 202308.03 |
| SENTIEON_TNHAPLOTYPER2 | sentieon | 202308.03 |
| SNPEFF_SNPEFF | snpeff | 5.1d |
| STRELKA_SINGLE | strelka | 2.9.10 |
| STRELKA_SOMATIC | strelka | 2.9.10 |
| TABIX_BGZIPTABIX | tabix | 1.2 |
| TABIX_TABIX | tabix | 1.2 |
| TABIX_VCF_FOR_ENTROPY | tabix | 1.2 |
| TIH_HRD_CALLING | hrd_calling | 0.2.0 |
| r-base | 4.3.3 | |
| VCFTOOLS_TSTV_COUNT | vcftools | 0.1.16 |
| WHATSHAP_MUTECT2 | whatshap | 2.8 |
| Workflow | Nextflow | 25.10.2 |
| nf-core/sarek | v3.5.0-g2a14cf2 |
nf-core/sarek Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/sarek
Methods
Data was processed using nf-core/sarek v3.5.0 (doi: 10.12688/f1000research.16665.2), (doi: 10.1093/nargab/lqae031), (doi: 10.5281/zenodo.3476425) 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' -output-dir 's3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_filtered_bams__2a14cf2e--20260209-153554' -r 2a14cf2ef8bdcf024597da8f2ac28d7549d387a0 -profile docker,eks,std_run,slack_test --input 's3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/samplesheets/samplesheet_cgp_atx_exp0001_tools_filtered_bams_from_daq.csv' --outdir 's3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_filtered_bams__2a14cf2e--20260209-153554' -name sarek-tools-daq-filtered-2a14cf2eReferences
- 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:
- 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.
nf-core/sarek Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/sarek
Input/output options
- input
- s3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/samplesheets/samplesheet_cgp_atx_exp0001_tools_filtered_bams_from_daq.csv
- outdir
- s3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_filtered_bams__2a14cf2e--20260209-153554
- step
- variant_calling
Main options
- intervals
- s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed
- nucleotides_per_second
- 15000
- tools
- sentieon_dedup,ngscheckmate,contamination,mutect2,tnseq,strelka,manta,msisensor2,ascat,cnvkit,facets,hla_optitype,tmb,hrd,whatshap,snpeff,merge,sentieon_haplotyper,haplotypecaller,chip_detection,indelentropy
- wes
- true
FASTQ Preprocessing
- save_trimmed
- true
- trim_fastq
- true
Preprocessing
- aligner
- sentieon-bwamem
- save_output_as_bam
- true
Variant Calling
- cf_chrom_len
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len
- 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
- pon
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/aih_blood_normal_36_pon.vcf.gz
- pon_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/aih_blood_normal_36_pon.vcf.gz.tbi
General reference genome options
- hlala_graph
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/HLA_LA/PRG_MHC_GRCh38_withIMGT_indexed/
- 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/
- xhla_chr6_bwa
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/xHLA/Sequence/BWAIndex/
- xhla_chr6_fai
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/xHLA/Sequence/chr6/hg38.chr6.fasta.fai
- xhla_chr6_fasta
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/xHLA/Sequence/chr6/hg38.chr6.fasta
- yara
- s3://natera-platform-sandbox/pipeline-resources/AIH/hla_typing/hla_index/
Reference genome options
- ascat_alleles
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
- ascat_genome
- hg38
- ascat_loci
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip
- ascat_loci_gc
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip
- ascat_loci_rt
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip
- 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
- bwa
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
- bwamem2
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
- chr_dir
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
- 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
- contam_bed
- s3://natera-platform-sandbox/platform-users/ralla/nfcore_rnafusion_resources/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed
- 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
- dragmap
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
- 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_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
- known_indels
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz
- known_indels_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi
- known_indels_vqsr
- --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
- known_snps
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz
- known_snps_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi
- known_snps_vqsr
- --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
- 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
- mappability
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
- ngscheckmate_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
- ngscheckmate_fastq_pt
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.pt
- probe_bed
- s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.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
- sentieon_dnascope_model
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
- seqtool_dbsnp
- s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
- seqtool_dbsnp_index
- s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
- 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/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.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/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_footprint.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.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/
Generic options
- task_job_queue
- Nextflow-OnDemand
Core Nextflow options
- configFiles
- N/A
- containerEngine
- docker
- launchDir
- /code
- profile
- docker,eks,std_run,slack_test
- projectDir
- /tmp/home/.nextflow/assets/rd-platform/bioinformatics/nextflow/sarek
- runName
- sarek-tools-daq-filtered-2a14cf2e
- userName
- nextflow
- workDir
- /natera-rnd-pltf-dev-nextflow-scratch-01/work
