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 2026-02-04, 10:02 UTC
based on data in:
/tmp/nxf.nEa9PonEyN
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 | 1018 | 17361 | 16747 | 30556 | 0 | 0 | 30556 | 30556 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 54 | 254 | 254 | 173 | 0 | 0 | 173 | 173 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 5 | 84 | 84 | 131 | 0 | 0 | 131 | 131 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.mutect2.filtered_custom.ann_snpEff_VEP.ann | 305 | 5569 | 5492 | 9005 | 0 | 0 | 9005 | 9005 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 305 | 5569 | 5492 | 9005 | 0 | 0 | 9005 | 9005 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 126 | 2566 | 2544 | 1825 | 0 | 0 | 1825 | 1825 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 464 | 12530 | 12196 | 17185 | 0 | 0 | 17185 | 17185 |
| 1029_032-T1-TDNA-1_23FC2GLT4_s01_vs_1029_032-N1-BDNA-1_2375WFLT3_s01.tnseq.filtered_custom.ann_snpEff_VEP.ann | 988 | 17973 | 17362 | 33061 | 0 | 0 | 33061 | 33061 |
| 1029_05O-N1-BDNA-1_2375WFLT3_s02.entropy.entropy_custom.ann_snpEff_VEP.ann | 54 | 222 | 222 | 137 | 0 | 0 | 137 | 137 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 48 | 235 | 235 | 147 | 0 | 0 | 147 | 148 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 11 | 11 | 17 | 0 | 0 | 17 | 17 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.mutect2.filtered_custom.ann_snpEff_VEP.ann | 245 | 4482 | 4425 | 5979 | 0 | 0 | 5979 | 5979 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 245 | 4482 | 4425 | 5979 | 0 | 0 | 5979 | 5979 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 108 | 1888 | 1879 | 1308 | 0 | 0 | 1308 | 1308 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 631 | 12729 | 12374 | 17036 | 0 | 0 | 17036 | 17036 |
| 1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02.tnseq.filtered_custom.ann_snpEff_VEP.ann | 886 | 17284 | 16701 | 28223 | 0 | 0 | 28223 | 28223 |
| 1029_0DT-N1-BDNA-1_2375WFLT3_s03.entropy.entropy_custom.ann_snpEff_VEP.ann | 1006 | 17410 | 16790 | 29566 | 0 | 0 | 29566 | 29566 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 61 | 271 | 271 | 173 | 0 | 0 | 173 | 174 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 62 | 62 | 86 | 0 | 0 | 86 | 86 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.mutect2.filtered_custom.ann_snpEff_VEP.ann | 327 | 5252 | 5189 | 9210 | 0 | 0 | 9210 | 9210 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 327 | 5252 | 5189 | 9210 | 0 | 0 | 9210 | 9210 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 129 | 2625 | 2606 | 1757 | 0 | 0 | 1757 | 1757 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 415 | 8998 | 8830 | 10472 | 0 | 0 | 10472 | 10472 |
| 1029_0DT-T1-TDNA-1_23FC2GLT4_s03_vs_1029_0DT-N1-BDNA-1_2375WFLT3_s03.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1014 | 18036 | 17422 | 32459 | 0 | 0 | 32459 | 32459 |
| 1029_0NX-N1-BDNA-1_2375WFLT3_s04.entropy.entropy_custom.ann_snpEff_VEP.ann | 1018 | 17940 | 17307 | 30147 | 0 | 0 | 30147 | 30147 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 68 | 264 | 264 | 187 | 0 | 0 | 187 | 187 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 3 | 106 | 106 | 158 | 0 | 0 | 158 | 160 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.mutect2.filtered_custom.ann_snpEff_VEP.ann | 332 | 5657 | 5585 | 9800 | 0 | 0 | 9800 | 9800 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 332 | 5657 | 5585 | 9800 | 0 | 0 | 9800 | 9800 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 144 | 2437 | 2424 | 1688 | 0 | 0 | 1688 | 1688 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 393 | 10026 | 9825 | 12296 | 0 | 0 | 12296 | 12296 |
| 1029_0NX-T1-TDNA-1_23FC2GLT4_s04_vs_1029_0NX-N1-BDNA-1_2375WFLT3_s04.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1027 | 18583 | 17953 | 34363 | 0 | 0 | 34363 | 34363 |
| 1029_1G0-N1-BDNA-1_2375WFLT3_s05.entropy.entropy_custom.ann_snpEff_VEP.ann | 1019 | 17444 | 16826 | 30706 | 0 | 0 | 30706 | 30706 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 41 | 252 | 252 | 166 | 0 | 0 | 166 | 166 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 14 | 119 | 119 | 125 | 0 | 0 | 125 | 125 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.mutect2.filtered_custom.ann_snpEff_VEP.ann | 654 | 13770 | 13423 | 22681 | 0 | 0 | 22681 | 22681 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 654 | 13770 | 13423 | 22681 | 0 | 0 | 22681 | 22681 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 176 | 3300 | 3263 | 2339 | 0 | 0 | 2339 | 2339 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 938 | 18361 | 17702 | 29774 | 0 | 0 | 29774 | 29774 |
| 1029_1G0-T1-TDNA-1_23FC2GLT4_s05_vs_1029_1G0-N1-BDNA-1_2375WFLT3_s05.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1338 | 22188 | 21273 | 48363 | 0 | 0 | 48363 | 48363 |
| 1029_1H5-N1-BDNA-1_2375WFLT3_s06.entropy.entropy_custom.ann_snpEff_VEP.ann | 991 | 17470 | 16845 | 29307 | 0 | 0 | 29307 | 29307 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 44 | 262 | 262 | 171 | 0 | 0 | 171 | 171 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 3 | 56 | 56 | 82 | 0 | 0 | 82 | 82 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.mutect2.filtered_custom.ann_snpEff_VEP.ann | 346 | 5776 | 5693 | 9028 | 0 | 0 | 9028 | 9028 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 346 | 5776 | 5693 | 9028 | 0 | 0 | 9028 | 9028 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 129 | 2722 | 2704 | 1953 | 0 | 0 | 1953 | 1953 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 562 | 13017 | 12650 | 17547 | 0 | 0 | 17547 | 17547 |
| 1029_1H5-T1-TDNA-1_23FC2GLT4_s06_vs_1029_1H5-N1-BDNA-1_2375WFLT3_s06.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1043 | 18405 | 17746 | 33633 | 0 | 0 | 33633 | 33633 |
| 1029_2IN-N1-BDNA-1_2375WFLT3_s07.entropy.entropy_custom.ann_snpEff_VEP.ann | 33 | 181 | 181 | 115 | 0 | 0 | 115 | 115 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 43 | 236 | 236 | 152 | 0 | 0 | 152 | 152 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 19 | 200 | 200 | 292 | 0 | 0 | 292 | 294 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.mutect2.filtered_custom.ann_snpEff_VEP.ann | 436 | 8734 | 8587 | 14497 | 0 | 0 | 14497 | 14497 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 436 | 8734 | 8587 | 14497 | 0 | 0 | 14497 | 14497 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 164 | 3225 | 3200 | 2298 | 0 | 0 | 2298 | 2298 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 556 | 12582 | 12275 | 16433 | 0 | 0 | 16433 | 16433 |
| 1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1154 | 19602 | 18900 | 40089 | 0 | 0 | 40089 | 40089 |
| 1029_2LI-N1-BDNA-1_2375WFLT3_s08.entropy.entropy_custom.ann_snpEff_VEP.ann | 35 | 196 | 196 | 131 | 0 | 0 | 131 | 131 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 40 | 235 | 235 | 157 | 0 | 0 | 157 | 157 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 58 | 58 | 68 | 0 | 0 | 68 | 69 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.filtered_custom.ann_snpEff_VEP.ann | 305 | 5926 | 5846 | 8796 | 0 | 0 | 8796 | 8796 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 305 | 5926 | 5846 | 8796 | 0 | 0 | 8796 | 8796 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 99 | 2333 | 2320 | 1596 | 0 | 0 | 1596 | 1596 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 275 | 8212 | 8073 | 9099 | 0 | 0 | 9099 | 9099 |
| 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.tnseq.filtered_custom.ann_snpEff_VEP.ann | 972 | 18139 | 17528 | 32996 | 0 | 0 | 32996 | 32996 |
| 1029_3N0-N1-BDNA-1_2375WFLT3_s09.entropy.entropy_custom.ann_snpEff_VEP.ann | 981 | 17107 | 16513 | 30341 | 0 | 0 | 30341 | 30341 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 62 | 239 | 239 | 159 | 0 | 0 | 159 | 159 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 68 | 68 | 93 | 0 | 0 | 93 | 94 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.mutect2.filtered_custom.ann_snpEff_VEP.ann | 425 | 8024 | 7883 | 13661 | 0 | 0 | 13661 | 13661 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 425 | 8024 | 7883 | 13661 | 0 | 0 | 13661 | 13661 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 140 | 2971 | 2946 | 2005 | 0 | 0 | 2005 | 2005 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 360 | 9587 | 9408 | 11170 | 0 | 0 | 11170 | 11170 |
| 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1128 | 19327 | 18626 | 39232 | 0 | 0 | 39232 | 39232 |
| 1029_3OH-N1-BDNA-1_2375WFLT3_s10.entropy.entropy_custom.ann_snpEff_VEP.ann | 995 | 17289 | 16695 | 29619 | 0 | 0 | 29619 | 29619 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 59 | 257 | 257 | 161 | 0 | 0 | 161 | 162 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 32 | 32 | 51 | 0 | 0 | 51 | 51 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.mutect2.filtered_custom.ann_snpEff_VEP.ann | 441 | 7019 | 6917 | 11241 | 0 | 0 | 11241 | 11241 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 441 | 7019 | 6917 | 11241 | 0 | 0 | 11241 | 11241 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 139 | 2851 | 2814 | 1903 | 0 | 0 | 1903 | 1903 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 294 | 8652 | 8506 | 9779 | 0 | 0 | 9779 | 9779 |
| 1029_3OH-T1-TDNA-1_23FC2GLT4_s10_vs_1029_3OH-N1-BDNA-1_2375WFLT3_s10.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1201 | 19050 | 18358 | 37077 | 0 | 0 | 37077 | 37077 |
| 1029_4J3-N1-BDNA-1_2375WFLT3_s11.entropy.entropy_custom.ann_snpEff_VEP.ann | 1007 | 17521 | 16906 | 30405 | 0 | 0 | 30405 | 30405 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 53 | 271 | 271 | 166 | 0 | 0 | 166 | 166 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 54 | 53 | 79 | 0 | 0 | 79 | 79 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.mutect2.filtered_custom.ann_snpEff_VEP.ann | 293 | 4959 | 4893 | 7842 | 0 | 0 | 7842 | 7842 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 293 | 4959 | 4893 | 7842 | 0 | 0 | 7842 | 7842 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 103 | 2228 | 2216 | 1515 | 0 | 0 | 1515 | 1515 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 347 | 8453 | 8290 | 10483 | 0 | 0 | 10483 | 10483 |
| 1029_4J3-T1-TDNA-1_23FC2GLT4_s11_vs_1029_4J3-N1-BDNA-1_2375WFLT3_s11.tnseq.filtered_custom.ann_snpEff_VEP.ann | 937 | 17710 | 17137 | 31049 | 0 | 0 | 31049 | 31049 |
| 1029_4Z2-N1-BDNA-1_2375WFLT3_s12.entropy.entropy_custom.ann_snpEff_VEP.ann | 1004 | 17272 | 16673 | 29878 | 0 | 0 | 29878 | 29878 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 45 | 227 | 226 | 137 | 0 | 0 | 137 | 137 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 82 | 82 | 104 | 0 | 0 | 104 | 104 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.mutect2.filtered_custom.ann_snpEff_VEP.ann | 704 | 14460 | 14056 | 23135 | 0 | 0 | 23135 | 23135 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 704 | 14460 | 14056 | 23135 | 0 | 0 | 23135 | 23135 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 180 | 3400 | 3382 | 2365 | 0 | 0 | 2365 | 2365 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 832 | 16974 | 16414 | 25231 | 0 | 0 | 25231 | 25231 |
| 1029_4Z2-T1-TDNA-1_23FC2GLT4_s12_vs_1029_4Z2-N1-BDNA-1_2375WFLT3_s12.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1388 | 22507 | 21550 | 48619 | 0 | 0 | 48619 | 48619 |
| 1029_56D-N1-BDNA-1_2375WFLT3_s13.entropy.entropy_custom.ann_snpEff_VEP.ann | 967 | 17367 | 16765 | 29631 | 0 | 0 | 29631 | 29631 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 37 | 238 | 238 | 148 | 0 | 0 | 148 | 148 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 4 | 62 | 62 | 66 | 0 | 0 | 66 | 68 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.mutect2.filtered_custom.ann_snpEff_VEP.ann | 358 | 7672 | 7559 | 11443 | 0 | 0 | 11443 | 11443 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 358 | 7672 | 7559 | 11443 | 0 | 0 | 11443 | 11443 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 101 | 2485 | 2467 | 1707 | 0 | 0 | 1707 | 1707 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 435 | 11807 | 11545 | 15688 | 0 | 0 | 15688 | 15688 |
| 1029_56D-T1-TDNA-1_23FC2GLT4_s13_vs_1029_56D-N1-BDNA-1_2375WFLT3_s13.tnseq.filtered_custom.ann_snpEff_VEP.ann | 966 | 18741 | 18100 | 34536 | 0 | 0 | 34536 | 34536 |
| 1029_5IX-N1-BDNA-1_2375WFLT3_s14.entropy.entropy_custom.ann_snpEff_VEP.ann | 1123 | 18717 | 18028 | 33166 | 0 | 0 | 33166 | 33166 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 70 | 253 | 253 | 156 | 0 | 0 | 156 | 157 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 20 | 20 | 24 | 0 | 0 | 24 | 25 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.mutect2.filtered_custom.ann_snpEff_VEP.ann | 507 | 10947 | 10726 | 14616 | 0 | 0 | 14616 | 14616 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 507 | 10947 | 10726 | 14616 | 0 | 0 | 14616 | 14616 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 124 | 2591 | 2567 | 1835 | 0 | 0 | 1835 | 1835 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 407 | 10310 | 10084 | 11695 | 0 | 0 | 11695 | 11695 |
| 1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1375 | 21923 | 21036 | 43513 | 0 | 0 | 43513 | 43513 |
| 1029_5O3-N1-BDNA-1_2375WFLT3_s15.entropy.entropy_custom.ann_snpEff_VEP.ann | 36 | 176 | 176 | 110 | 0 | 0 | 110 | 110 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 45 | 241 | 241 | 152 | 0 | 0 | 152 | 152 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 60 | 60 | 64 | 0 | 0 | 64 | 65 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.mutect2.filtered_custom.ann_snpEff_VEP.ann | 771 | 15155 | 14727 | 23570 | 0 | 0 | 23570 | 23570 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 771 | 15155 | 14727 | 23570 | 0 | 0 | 23570 | 23570 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 197 | 3521 | 3504 | 2556 | 0 | 0 | 2556 | 2556 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1246 | 21146 | 20303 | 38190 | 0 | 0 | 38190 | 38190 |
| 1029_5O3-T1-TDNA-1_23FC2GLT4_s15_vs_1029_5O3-N1-BDNA-1_2375WFLT3_s15.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1389 | 22798 | 21830 | 47637 | 0 | 0 | 47637 | 47637 |
| 1029_7Y1-N1-BDNA-1_2375WFLT3_s16.entropy.entropy_custom.ann_snpEff_VEP.ann | 25 | 176 | 176 | 114 | 0 | 0 | 114 | 114 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 45 | 222 | 222 | 140 | 0 | 0 | 140 | 140 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 3 | 88 | 88 | 100 | 0 | 0 | 100 | 101 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.mutect2.filtered_custom.ann_snpEff_VEP.ann | 1099 | 22083 | 21213 | 42657 | 0 | 0 | 42657 | 42657 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 1099 | 22083 | 21213 | 42657 | 0 | 0 | 42657 | 42657 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 173 | 2930 | 2894 | 2063 | 0 | 0 | 2063 | 2063 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 712 | 16223 | 15717 | 22462 | 0 | 0 | 22462 | 22462 |
| 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1797 | 26960 | 25612 | 69693 | 0 | 0 | 69693 | 69693 |
| 1029_8AV-N1-BDNA-1_2375WFLT3_s17.entropy.entropy_custom.ann_snpEff_VEP.ann | 28 | 173 | 173 | 137 | 0 | 0 | 137 | 137 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 47 | 238 | 238 | 180 | 0 | 0 | 180 | 180 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 81 | 81 | 110 | 0 | 0 | 110 | 110 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.mutect2.filtered_custom.ann_snpEff_VEP.ann | 303 | 5170 | 5092 | 8788 | 0 | 0 | 8788 | 8788 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 303 | 5170 | 5092 | 8788 | 0 | 0 | 8788 | 8788 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 138 | 2431 | 2412 | 1685 | 0 | 0 | 1685 | 1685 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 503 | 11274 | 10996 | 15863 | 0 | 0 | 15863 | 15863 |
| 1029_8AV-T1-TDNA-1_23FC2GLT4_s17_vs_1029_8AV-N1-BDNA-1_2375WFLT3_s17.tnseq.filtered_custom.ann_snpEff_VEP.ann | 973 | 17879 | 17286 | 31998 | 0 | 0 | 31998 | 31998 |
| 1029_8BO-N1-BDNA-1_2375WFLT3_s18.entropy.entropy_custom.ann_snpEff_VEP.ann | 985 | 17426 | 16831 | 29703 | 0 | 0 | 29703 | 29703 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 41 | 239 | 239 | 157 | 0 | 0 | 157 | 157 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 7 | 71 | 71 | 74 | 0 | 0 | 74 | 74 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.mutect2.filtered_custom.ann_snpEff_VEP.ann | 963 | 19207 | 18550 | 31856 | 0 | 0 | 31856 | 31856 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 963 | 19207 | 18550 | 31856 | 0 | 0 | 31856 | 31856 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 143 | 2500 | 2486 | 1674 | 0 | 0 | 1674 | 1674 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 350 | 9757 | 9563 | 10982 | 0 | 0 | 10982 | 10982 |
| 1029_8BO-T1-TDNA-1_23FC2GLT4_s18_vs_1029_8BO-N1-BDNA-1_2375WFLT3_s18.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1695 | 25373 | 24175 | 59648 | 0 | 0 | 59648 | 59648 |
| 1029_8OI-N1-BDNA-1_2375WFLT3_s19.entropy.entropy_custom.ann_snpEff_VEP.ann | 1009 | 17301 | 16696 | 29714 | 0 | 0 | 29714 | 29714 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 39 | 241 | 241 | 171 | 0 | 0 | 171 | 171 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 5 | 124 | 124 | 171 | 0 | 0 | 171 | 172 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.mutect2.filtered_custom.ann_snpEff_VEP.ann | 586 | 11675 | 11455 | 18983 | 0 | 0 | 18983 | 18983 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 586 | 11675 | 11455 | 18983 | 0 | 0 | 18983 | 18983 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 176 | 3199 | 3181 | 2301 | 0 | 0 | 2301 | 2301 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 656 | 14474 | 14064 | 20004 | 0 | 0 | 20004 | 20004 |
| 1029_8OI-T1-TDNA-1_23FC2GLT4_s19_vs_1029_8OI-N1-BDNA-1_2375WFLT3_s19.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1296 | 21056 | 20249 | 45413 | 0 | 0 | 45413 | 45413 |
| 1029_BA0-N2-BDNA-1_2375WFLT3_s20.entropy.entropy_custom.ann_snpEff_VEP.ann | 1015 | 17895 | 17252 | 30922 | 0 | 0 | 30922 | 30922 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 38 | 270 | 270 | 176 | 0 | 0 | 176 | 176 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 58 | 58 | 73 | 0 | 0 | 73 | 73 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.mutect2.filtered_custom.ann_snpEff_VEP.ann | 260 | 4338 | 4282 | 6790 | 0 | 0 | 6790 | 6790 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 260 | 4338 | 4282 | 6790 | 0 | 0 | 6790 | 6790 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 104 | 2400 | 2383 | 1693 | 0 | 0 | 1693 | 1693 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 421 | 9473 | 9260 | 12330 | 0 | 0 | 12330 | 12330 |
| 1029_BA0-T1-TDNA-1_23FC2GLT4_s20_vs_1029_BA0-N2-BDNA-1_2375WFLT3_s20.tnseq.filtered_custom.ann_snpEff_VEP.ann | 926 | 17849 | 17245 | 30578 | 0 | 0 | 30578 | 30578 |
| 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.entropy.entropy_custom.ann_snpEff_VEP.ann | 995 | 17355 | 16740 | 30355 | 0 | 0 | 30355 | 30355 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 54 | 196 | 196 | 127 | 0 | 0 | 127 | 127 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 28 | 28 | 31 | 0 | 0 | 31 | 31 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.filtered_custom.ann_snpEff_VEP.ann | 176 | 5318 | 5277 | 4581 | 0 | 0 | 4581 | 4581 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 176 | 5318 | 5277 | 4581 | 0 | 0 | 4581 | 4581 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 80 | 1612 | 1593 | 1580 | 0 | 0 | 1580 | 1580 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 701 | 18347 | 17712 | 28081 | 0 | 0 | 28081 | 28081 |
| 1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tnseq.filtered_custom.ann_snpEff_VEP.ann | 822 | 17391 | 16813 | 26157 | 0 | 0 | 26157 | 26157 |
| 1029_BBOC-N1-BDNA-1_2375WFLT3_s22.entropy.entropy_custom.ann_snpEff_VEP.ann | 1010 | 17457 | 16860 | 30966 | 0 | 0 | 30966 | 30966 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 31 | 259 | 259 | 178 | 0 | 0 | 178 | 178 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 55 | 55 | 63 | 0 | 0 | 63 | 64 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.mutect2.filtered_custom.ann_snpEff_VEP.ann | 291 | 5200 | 5128 | 8719 | 0 | 0 | 8719 | 8719 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 291 | 5200 | 5128 | 8719 | 0 | 0 | 8719 | 8719 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 105 | 2517 | 2497 | 1747 | 0 | 0 | 1747 | 1747 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 554 | 11997 | 11682 | 17195 | 0 | 0 | 17195 | 17195 |
| 1029_BBOC-T1-TDNA-1_23FC2GLT4_s22_vs_1029_BBOC-N1-BDNA-1_2375WFLT3_s22.tnseq.filtered_custom.ann_snpEff_VEP.ann | 950 | 17815 | 17242 | 32706 | 0 | 0 | 32706 | 32706 |
| 1029_BBS1-N1-BDNA-1_2375WFLT3_s23.entropy.entropy_custom.ann_snpEff_VEP.ann | 16 | 148 | 148 | 107 | 0 | 0 | 107 | 107 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 24 | 246 | 246 | 171 | 0 | 0 | 171 | 171 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 73 | 73 | 95 | 0 | 0 | 95 | 96 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.filtered_custom.ann_snpEff_VEP.ann | 351 | 5757 | 5678 | 10068 | 0 | 0 | 10068 | 10068 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 351 | 5757 | 5678 | 10068 | 0 | 0 | 10068 | 10068 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 161 | 2920 | 2896 | 2015 | 0 | 0 | 2015 | 2015 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 400 | 10104 | 9884 | 12715 | 0 | 0 | 12715 | 12715 |
| 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1026 | 18312 | 17668 | 33962 | 0 | 0 | 33962 | 33962 |
| 1029_BCB6-N1-BDNA-1_2375WFLT3_s24.entropy.entropy_custom.ann_snpEff_VEP.ann | 43 | 211 | 211 | 133 | 0 | 0 | 133 | 133 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 37 | 210 | 210 | 145 | 0 | 0 | 145 | 145 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 6 | 158 | 157 | 176 | 0 | 0 | 176 | 176 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.mutect2.filtered_custom.ann_snpEff_VEP.ann | 1126 | 21558 | 20717 | 43313 | 0 | 0 | 43313 | 43313 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 1126 | 21558 | 20717 | 43313 | 0 | 0 | 43313 | 43313 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 162 | 3037 | 3007 | 2150 | 0 | 0 | 2150 | 2150 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 547 | 12703 | 12372 | 16487 | 0 | 0 | 16487 | 16487 |
| 1029_BCB6-T1-TDNA-1_23FC2GLT4_s24_vs_1029_BCB6-N1-BDNA-1_2375WFLT3_s24.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1845 | 26670 | 25333 | 70056 | 0 | 0 | 70056 | 70056 |
| 1029_BCTO-N1-BDNA-1_2375WFLT3_s25.entropy.entropy_custom.ann_snpEff_VEP.ann | 1011 | 17450 | 16838 | 29446 | 0 | 0 | 29446 | 29446 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 38 | 225 | 225 | 141 | 0 | 0 | 141 | 141 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 22 | 131 | 130 | 94 | 0 | 0 | 94 | 94 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.mutect2.filtered_custom.ann_snpEff_VEP.ann | 883 | 16412 | 15911 | 27298 | 0 | 0 | 27298 | 27298 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 883 | 16412 | 15911 | 27298 | 0 | 0 | 27298 | 27298 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 253 | 3787 | 3747 | 3097 | 0 | 0 | 3097 | 3097 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1296 | 22341 | 21438 | 42174 | 0 | 0 | 42174 | 42174 |
| 1029_BCTO-T1-TDNA-1_23FC2GLT4_s25_vs_1029_BCTO-N1-BDNA-1_2375WFLT3_s25.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1514 | 23589 | 22551 | 51955 | 0 | 0 | 51955 | 51955 |
| 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.entropy.entropy_custom.ann_snpEff_VEP.ann | 1036 | 17834 | 17203 | 31208 | 0 | 0 | 31208 | 31208 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 40 | 237 | 237 | 158 | 0 | 0 | 158 | 159 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 48 | 48 | 39 | 0 | 0 | 39 | 39 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.mutect2.filtered_custom.ann_snpEff_VEP.ann | 310 | 5074 | 5012 | 7148 | 0 | 0 | 7148 | 7148 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 310 | 5074 | 5012 | 7148 | 0 | 0 | 7148 | 7148 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 141 | 2612 | 2591 | 1895 | 0 | 0 | 1895 | 1895 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 555 | 12411 | 12064 | 16555 | 0 | 0 | 16555 | 16555 |
| 1029_BDOZ-T1-TDNA-1_23FC2GLT4_s26_vs_1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1054 | 18416 | 17769 | 32548 | 0 | 0 | 32548 | 32548 |
| 1029_BF2U-N1-BDNA-1_2375WFLT3_s27.entropy.entropy_custom.ann_snpEff_VEP.ann | 1013 | 17134 | 16537 | 29723 | 0 | 0 | 29723 | 29723 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 16 | 173 | 173 | 117 | 0 | 0 | 117 | 117 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 21 | 21 | 29 | 0 | 0 | 29 | 29 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.mutect2.filtered_custom.ann_snpEff_VEP.ann | 290 | 4625 | 4574 | 6566 | 0 | 0 | 6566 | 6566 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 290 | 4625 | 4574 | 6566 | 0 | 0 | 6566 | 6566 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 93 | 2061 | 2046 | 1421 | 0 | 0 | 1421 | 1421 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 222 | 6337 | 6259 | 6126 | 0 | 0 | 6126 | 6126 |
| 1029_BF2U-T1-TDNA-1_23FC2GLT4_s27_vs_1029_BF2U-N1-BDNA-1_2375WFLT3_s27.tnseq.filtered_custom.ann_snpEff_VEP.ann | 945 | 17328 | 16761 | 29414 | 0 | 0 | 29414 | 29414 |
| 1029_BFKM-N1-BDNA-1_2375WFLT3_s28.entropy.entropy_custom.ann_snpEff_VEP.ann | 34 | 174 | 174 | 130 | 0 | 0 | 130 | 130 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 29 | 215 | 215 | 156 | 0 | 0 | 156 | 156 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 7 | 142 | 141 | 185 | 0 | 0 | 185 | 187 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.mutect2.filtered_custom.ann_snpEff_VEP.ann | 773 | 15882 | 15448 | 28671 | 0 | 0 | 28671 | 28671 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 773 | 15882 | 15448 | 28671 | 0 | 0 | 28671 | 28671 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 215 | 3687 | 3654 | 2715 | 0 | 0 | 2715 | 2715 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 597 | 14102 | 13726 | 19386 | 0 | 0 | 19386 | 19386 |
| 1029_BFKM-T1-TDNA-1_23FC2GLT4_s28_vs_1029_BFKM-N1-BDNA-1_2375WFLT3_s28.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1523 | 23399 | 22402 | 55893 | 0 | 0 | 55893 | 55893 |
| 1029_BG5-N1-BDNA-1_2375WFLT3_s29.entropy.entropy_custom.ann_snpEff_VEP.ann | 33 | 180 | 180 | 122 | 0 | 0 | 122 | 122 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 32 | 173 | 173 | 124 | 0 | 0 | 124 | 124 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 18 | 18 | 24 | 0 | 0 | 24 | 24 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.filtered_custom.ann_snpEff_VEP.ann | 29 | 1210 | 1206 | 1109 | 0 | 0 | 1109 | 1109 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 29 | 1210 | 1206 | 1109 | 0 | 0 | 1109 | 1109 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 184 | 2766 | 2738 | 2501 | 0 | 0 | 2501 | 2501 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 813 | 18852 | 18224 | 25399 | 0 | 0 | 25399 | 25399 |
| 1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tnseq.filtered_custom.ann_snpEff_VEP.ann | 674 | 15486 | 15021 | 22202 | 0 | 0 | 22202 | 22202 |
| 1029_BGFD-N1-BDNA-1_2375WFLT3_s30.entropy.entropy_custom.ann_snpEff_VEP.ann | 957 | 17241 | 16638 | 29350 | 0 | 0 | 29350 | 29350 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 57 | 184 | 184 | 119 | 0 | 0 | 119 | 119 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 4 | 63 | 63 | 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 | 876 | 18787 | 18164 | 32988 | 0 | 0 | 32988 | 32988 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 876 | 18787 | 18164 | 32988 | 0 | 0 | 32988 | 32988 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 193 | 3309 | 3288 | 2345 | 0 | 0 | 2345 | 2345 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 316 | 10030 | 9848 | 11192 | 0 | 0 | 11192 | 11192 |
| 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1583 | 25062 | 23939 | 60032 | 0 | 0 | 60032 | 60032 |
| 1029_BGMF-N1-BDNA-1_2375WFLT3_s31.entropy.entropy_custom.ann_snpEff_VEP.ann | 30 | 188 | 188 | 128 | 0 | 0 | 128 | 128 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 43 | 264 | 264 | 183 | 0 | 0 | 183 | 183 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 36 | 36 | 50 | 0 | 0 | 50 | 54 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.mutect2.filtered_custom.ann_snpEff_VEP.ann | 280 | 4516 | 4461 | 7316 | 0 | 0 | 7316 | 7316 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 280 | 4516 | 4461 | 7316 | 0 | 0 | 7316 | 7316 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 92 | 2004 | 1992 | 1381 | 0 | 0 | 1381 | 1381 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 366 | 8191 | 8046 | 10028 | 0 | 0 | 10028 | 10028 |
| 1029_BGMF-T1-TDNA-1_23FC2GLT4_s31_vs_1029_BGMF-N1-BDNA-1_2375WFLT3_s31.tnseq.filtered_custom.ann_snpEff_VEP.ann | 944 | 17434 | 16841 | 30979 | 0 | 0 | 30979 | 30979 |
| 1029_BICA-N1-BDNA-1_2375WFLT3_s32.entropy.entropy_custom.ann_snpEff_VEP.ann | 43 | 195 | 195 | 153 | 0 | 0 | 153 | 153 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 31 | 290 | 290 | 243 | 0 | 0 | 243 | 243 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 7 | 75 | 75 | 92 | 0 | 0 | 92 | 92 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.filtered_custom.ann_snpEff_VEP.ann | 586 | 13622 | 13315 | 22211 | 0 | 0 | 22211 | 22211 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 586 | 13622 | 13315 | 22211 | 0 | 0 | 22211 | 22211 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 111 | 2380 | 2370 | 1723 | 0 | 0 | 1723 | 1723 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 545 | 14951 | 14598 | 22356 | 0 | 0 | 22356 | 22356 |
| 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1242 | 21628 | 20802 | 46124 | 0 | 0 | 46124 | 46124 |
| 1029_BIHC-N1-BDNA-1_2375WFLT3_s33.entropy.entropy_custom.ann_snpEff_VEP.ann | 1013 | 17362 | 16760 | 29912 | 0 | 0 | 29912 | 29912 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 40 | 250 | 250 | 175 | 0 | 0 | 175 | 175 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 5 | 70 | 70 | 91 | 0 | 0 | 91 | 92 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.mutect2.filtered_custom.ann_snpEff_VEP.ann | 359 | 5957 | 5880 | 8615 | 0 | 0 | 8615 | 8615 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 359 | 5957 | 5880 | 8615 | 0 | 0 | 8615 | 8615 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 131 | 2833 | 2823 | 1944 | 0 | 0 | 1944 | 1944 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 278 | 7726 | 7614 | 8207 | 0 | 0 | 8207 | 8207 |
| 1029_BIHC-T1-TDNA-1_23FC2GLT4_s34_vs_1029_BIHC-N1-BDNA-1_2375WFLT3_s33.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1057 | 18263 | 17640 | 32289 | 0 | 0 | 32289 | 32289 |
| 1029_BIHO-N1-BDNA-1_2375WFLT3_s34.entropy.entropy_custom.ann_snpEff_VEP.ann | 32 | 188 | 188 | 134 | 0 | 0 | 134 | 134 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 31 | 312 | 312 | 226 | 0 | 0 | 226 | 226 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 8 | 84 | 84 | 103 | 0 | 0 | 103 | 103 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.mutect2.filtered_custom.ann_snpEff_VEP.ann | 321 | 6279 | 6201 | 10086 | 0 | 0 | 10086 | 10086 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 321 | 6279 | 6201 | 10086 | 0 | 0 | 10086 | 10086 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 87 | 2015 | 2006 | 1407 | 0 | 0 | 1407 | 1407 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 345 | 9356 | 9176 | 12655 | 0 | 0 | 12655 | 12655 |
| 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.tnseq.filtered_custom.ann_snpEff_VEP.ann | 969 | 18019 | 17414 | 33325 | 0 | 0 | 33325 | 33325 |
| 1029_BJH0-N1-BDNA-1_2375WFLT3_s35.entropy.entropy_custom.ann_snpEff_VEP.ann | 1017 | 17417 | 16799 | 29400 | 0 | 0 | 29400 | 29400 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 30 | 201 | 201 | 133 | 0 | 0 | 133 | 133 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 64 | 64 | 77 | 0 | 0 | 77 | 77 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.mutect2.filtered_custom.ann_snpEff_VEP.ann | 853 | 18287 | 17697 | 30924 | 0 | 0 | 30924 | 30924 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 853 | 18287 | 17697 | 30924 | 0 | 0 | 30924 | 30924 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 178 | 3097 | 3069 | 2191 | 0 | 0 | 2191 | 2191 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 441 | 11123 | 10891 | 13499 | 0 | 0 | 13499 | 13499 |
| 1029_BJH0-T1-TDNA-1_23FC2GLT4_s36_vs_1029_BJH0-N1-BDNA-1_2375WFLT3_s35.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1594 | 24698 | 23548 | 57998 | 0 | 0 | 57998 | 57998 |
| 1029_BK2H-N1-BDNA-1_2375WFLT3_s36.entropy.entropy_custom.ann_snpEff_VEP.ann | 1022 | 17590 | 16953 | 30290 | 0 | 0 | 30290 | 30290 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 42 | 257 | 257 | 163 | 0 | 0 | 163 | 163 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 33 | 94 | 94 | 105 | 0 | 0 | 105 | 106 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.filtered_custom.ann_snpEff_VEP.ann | 652 | 13411 | 13075 | 20729 | 0 | 0 | 20729 | 20729 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 652 | 13411 | 13075 | 20729 | 0 | 0 | 20729 | 20729 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 186 | 3369 | 3340 | 2472 | 0 | 0 | 2472 | 2472 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1180 | 20526 | 19737 | 37072 | 0 | 0 | 37072 | 37072 |
| 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1271 | 21845 | 20960 | 44553 | 0 | 0 | 44553 | 44553 |
| 1029_BLH5-N1-BDNA-1_2375WFLT3_s37.entropy.entropy_custom.ann_snpEff_VEP.ann | 1032 | 17772 | 17113 | 30071 | 0 | 0 | 30071 | 30071 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 53 | 255 | 255 | 180 | 0 | 0 | 180 | 180 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 69 | 69 | 93 | 0 | 0 | 93 | 93 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.mutect2.filtered_custom.ann_snpEff_VEP.ann | 311 | 5447 | 5372 | 8439 | 0 | 0 | 8439 | 8439 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 311 | 5447 | 5372 | 8439 | 0 | 0 | 8439 | 8439 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 123 | 2619 | 2602 | 1787 | 0 | 0 | 1787 | 1787 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 529 | 11233 | 10979 | 14112 | 0 | 0 | 14112 | 14112 |
| 1029_BLH5-T1-TDNA-1_23FC2GLT4_s38_vs_1029_BLH5-N1-BDNA-1_2375WFLT3_s37.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1015 | 18342 | 17681 | 33006 | 0 | 0 | 33006 | 33006 |
| 1029_BLU1-N1-BDNA-1_2375WFLT3_s38.entropy.entropy_custom.ann_snpEff_VEP.ann | 963 | 17265 | 16668 | 28635 | 0 | 0 | 28635 | 28635 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 60 | 263 | 263 | 164 | 0 | 0 | 164 | 164 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 42 | 42 | 52 | 0 | 0 | 52 | 53 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.mutect2.filtered_custom.ann_snpEff_VEP.ann | 267 | 4460 | 4408 | 7166 | 0 | 0 | 7166 | 7166 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 267 | 4460 | 4408 | 7166 | 0 | 0 | 7166 | 7166 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 97 | 2121 | 2110 | 1426 | 0 | 0 | 1426 | 1426 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 204 | 6172 | 6098 | 6839 | 0 | 0 | 6839 | 6839 |
| 1029_BLU1-T1-TDNA-1_23FC2GLT4_s39_vs_1029_BLU1-N1-BDNA-1_2375WFLT3_s38.tnseq.filtered_custom.ann_snpEff_VEP.ann | 917 | 17381 | 16820 | 29661 | 0 | 0 | 29661 | 29661 |
| 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.entropy.entropy_custom.ann_snpEff_VEP.ann | 1021 | 17307 | 16705 | 30418 | 0 | 0 | 30418 | 30418 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 57 | 235 | 235 | 171 | 0 | 0 | 171 | 171 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 2 | 75 | 75 | 102 | 0 | 0 | 102 | 104 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.mutect2.filtered_custom.ann_snpEff_VEP.ann | 323 | 6024 | 5941 | 9419 | 0 | 0 | 9419 | 9419 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 323 | 6024 | 5941 | 9419 | 0 | 0 | 9419 | 9419 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 138 | 2753 | 2734 | 1973 | 0 | 0 | 1973 | 1973 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 594 | 12757 | 12400 | 17301 | 0 | 0 | 17301 | 17301 |
| 1029_BN9Y-T1-TDNA-1_23FC2GLT4_s40_vs_1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.tnseq.filtered_custom.ann_snpEff_VEP.ann | 994 | 18138 | 17520 | 33262 | 0 | 0 | 33262 | 33262 |
| 1029_BNG8-N1-BDNA-1_2375WFLT3_s40.entropy.entropy_custom.ann_snpEff_VEP.ann | 989 | 17616 | 17001 | 29692 | 0 | 0 | 29692 | 29692 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 45 | 200 | 200 | 114 | 0 | 0 | 114 | 114 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 4 | 159 | 159 | 214 | 0 | 0 | 214 | 215 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.mutect2.filtered_custom.ann_snpEff_VEP.ann | 586 | 11323 | 11074 | 21242 | 0 | 0 | 21242 | 21242 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 586 | 11323 | 11074 | 21242 | 0 | 0 | 21242 | 21242 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 162 | 2906 | 2885 | 2061 | 0 | 0 | 2061 | 2061 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 217 | 7250 | 7125 | 8072 | 0 | 0 | 8072 | 8072 |
| 1029_BNG8-T1-TDNA-1_23FC2GLT4_s41_vs_1029_BNG8-N1-BDNA-1_2375WFLT3_s40.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1385 | 21542 | 20651 | 48660 | 0 | 0 | 48660 | 48660 |
| 1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.entropy.entropy_custom.ann_snpEff_VEP.ann | 966 | 17532 | 16945 | 29236 | 0 | 0 | 29236 | 29236 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 40 | 245 | 245 | 165 | 0 | 0 | 165 | 165 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 80 | 80 | 112 | 0 | 0 | 112 | 114 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.mutect2.filtered_custom.ann_snpEff_VEP.ann | 252 | 4063 | 4008 | 7100 | 0 | 0 | 7100 | 7100 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 252 | 4063 | 4008 | 7100 | 0 | 0 | 7100 | 7100 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 91 | 1843 | 1831 | 1267 | 0 | 0 | 1267 | 1267 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 271 | 7000 | 6899 | 8027 | 0 | 0 | 8027 | 8027 |
| 1029_BO4Y-T1-TDNA-1_23FC2GLT4_s42_vs_1029_BO4Y-N1-BDNA-1_2375WFLT3_s41.tnseq.filtered_custom.ann_snpEff_VEP.ann | 883 | 17423 | 16878 | 30167 | 0 | 0 | 30167 | 30167 |
| 1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.entropy.entropy_custom.ann_snpEff_VEP.ann | 982 | 17380 | 16772 | 29209 | 0 | 0 | 29209 | 29209 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 44 | 242 | 242 | 188 | 0 | 0 | 188 | 188 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 17 | 84 | 84 | 90 | 0 | 0 | 90 | 90 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.mutect2.filtered_custom.ann_snpEff_VEP.ann | 708 | 14931 | 14541 | 23118 | 0 | 0 | 23118 | 23118 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 708 | 14931 | 14541 | 23118 | 0 | 0 | 23118 | 23118 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 183 | 3185 | 3152 | 2407 | 0 | 0 | 2407 | 2407 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 1205 | 20752 | 19975 | 38521 | 0 | 0 | 38521 | 38521 |
| 1029_BOHJ-T1-TDNA-1_23FC2GLT4_s43_vs_1029_BOHJ-N1-BDNA-1_2375WFLT3_s42.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1295 | 22288 | 21403 | 46455 | 0 | 0 | 46455 | 46455 |
| 1029_BOSD-N1-BDNA-1_2375WFLT3_s43.entropy.entropy_custom.ann_snpEff_VEP.ann | 997 | 17339 | 16735 | 29847 | 0 | 0 | 29847 | 29847 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 38 | 255 | 255 | 163 | 0 | 0 | 163 | 164 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 0 | 80 | 80 | 104 | 0 | 0 | 104 | 105 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.mutect2.filtered_custom.ann_snpEff_VEP.ann | 306 | 6236 | 6150 | 9213 | 0 | 0 | 9213 | 9213 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 306 | 6236 | 6150 | 9213 | 0 | 0 | 9213 | 9213 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 145 | 2799 | 2775 | 1976 | 0 | 0 | 1976 | 1976 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 429 | 10491 | 10256 | 13463 | 0 | 0 | 13463 | 13463 |
| 1029_BOSD-T1-TDNA-1_23FC2GLT4_s44_vs_1029_BOSD-N1-BDNA-1_2375WFLT3_s43.tnseq.filtered_custom.ann_snpEff_VEP.ann | 959 | 18163 | 17534 | 32301 | 0 | 0 | 32301 | 32301 |
| 1029_BP21-N1-BDNA-1_2375WFLT3_s44.entropy.entropy_custom.ann_snpEff_VEP.ann | 50 | 186 | 186 | 153 | 0 | 0 | 153 | 153 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.manta.diploid_sv_custom.ann_snpEff_VEP.ann | 53 | 217 | 217 | 176 | 0 | 0 | 176 | 176 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.manta.somatic_sv_custom.ann_snpEff_VEP.ann | 1 | 66 | 66 | 77 | 0 | 0 | 77 | 78 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.mutect2.filtered_custom.ann_snpEff_VEP.ann | 323 | 5731 | 5659 | 8803 | 0 | 0 | 8803 | 8803 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann | 323 | 5731 | 5659 | 8803 | 0 | 0 | 8803 | 8803 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.strelka.somatic_indels_custom.ann_snpEff_VEP.ann | 86 | 1990 | 1979 | 1344 | 0 | 0 | 1344 | 1344 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann | 261 | 7582 | 7457 | 7761 | 0 | 0 | 7761 | 7761 |
| 1029_BP21-T1-TDNA-1_23FC2GLT4_s45_vs_1029_BP21-N1-BDNA-1_2375WFLT3_s44.tnseq.filtered_custom.ann_snpEff_VEP.ann | 1025 | 18423 | 17808 | 33485 | 0 | 0 | 33485 | 33485 |
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 | |
| 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 |
| 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 |
| 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-g8a99ba0 |
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_bams__8a99ba01--20260203-171151' -r 8a99ba012b42a28851320415f0be51c2790a8739 -profile docker,eks,std_run --input 's3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/samplesheets/samplesheet_cgp_atx_exp0001_tools_recal_bams_from_daq.csv' --outdir 's3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_bams__8a99ba01--20260203-171151' -name sarek-tools-daq-8a99ba01References
- 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_recal_bams_from_daq.csv
- outdir
- s3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_bams__8a99ba01--20260203-171151
- 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,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
- projectDir
- /tmp/home/.nextflow/assets/rd-platform/bioinformatics/nextflow/sarek
- runName
- sarek-tools-daq-8a99ba01
- userName
- nextflow
- workDir
- /natera-rnd-pltf-dev-nextflow-scratch-01/work
