Sample python aggregate_qc_metrics bcftools tabix samtools cnvkit facets conpair numpy gatk cyvcf2 deepvariant ensemblvep lightgbm bedtools scipy pysam manta gatk4 mimsi mosdepth msisensor2 n7_cosmic_sigs r-base scarHRD sentieon snpeff soma-cnv htslib strelka hrd_calling variant_qc_to_csv vcftools whatshap altera/sarek Nextflow
AGGREGATE_VARIANT_QC 3.12.6 2.0.0
ANNOTATE_BED_INFO 1.22
BCFTOOLS_ANNOTATE 1.2
BCFTOOLS_CONCAT 1.2
BCFTOOLS_MPILEUP 1.2
BCFTOOLS_QUERY 1.22
BCFTOOLS_STATS 1.2
BGZIPTABIX_GERMLINE_CNV 1.2
CNVKIT_BATCH 1.17 0.9.10
CNVKIT_CALL 0.9.10
CNVKIT_EXPORT 0.9.10
CNVKIT_GENEMETRICS 0.9.10
CNV_FACETS 0.6.2
CONCAT_WHATSHAP_TNSEQ_VCFS 1.2
CONCAT_WHATSHAP_VCFS 1.2
CONPAIR_CONTAMINATION 3.8.20 1.0 1.24.4
CONPAIR_PILEUP 3.8.20 1.0 4.6.2.0 Using
DIFF_DV_SENTIEON 3.11.14 0.31.1
DV_RESCUE 1.6.1
ENSEMBLVEP_VEP 113.0
EXTRACT_CHROMOSOMES 1.22
EXTRACT_CHROMOSOMES_TNSEQ 1.22
GT_CORRECTION 3.11.14 0.31.1 4.6.0 2.31.1
HARD_FILTER_VCF 3.9.15
INDEL_ENTROPY_ANNOTATION 3.13.11 2.4.0 1.16.3 0.23.3
LABEL_HOTSPOTS 3.9.15
MANTA_SOMATIC 1.6.0
MERGE_FORCECALLED 1.22
MERGE_SENTIEON_HAPLOTYPER_VCFS 4.5.0.0
MERGE_STRELKA_INDELS 4.5.0.0
MERGE_STRELKA_SNVS 4.5.0.0
MIMSI_ANALYZE 0.4.5.1
MSISENSOR2_MSI 0.1
Mosdepth 0.3.8
N7_COSMIC_SIGS 0.0.1 4.3.3
PREP_STRELKA_INDEL 1.22
PREP_TNSEQ_SNV 1.22
SAMTOOLS_MPILEUP 1.21
SAMTOOLS_STATS 1.21
SCARHRD 0.6.2
SENTIEON_FORCECALL 202308.03
SENTIEON_HAPLOTYPER 202308.03
SENTIEON_HAPLOTYPER_RF_FILTER 3.11.14 0.31.1 4.6.0 2.31.1
SENTIEON_TNFILTER 202308.03
SENTIEON_TNHAPLOTYPER2 202308.03
SNPEFF_SNPEFF 5.1d
SOMA_CNV_ALLELE_COUNTS 20260604-3cb5ec5
SOMA_CNV_BGZIP_TABIX 1.21
SOMA_CNV_CALL 20260604-3cb5ec5
SOMA_CNV_NORMALIZE 20260604-3cb5ec5
SOMA_CNV_PROBE_COUNTS 20260604-3cb5ec5
SPLIT_MULTIALLELIC 1.22
STRELKA_SOMATIC 2.9.10
TABIX_BGZIPTABIX 1.2
TABIX_TABIX 1.2
TABIX_VEP 1.2
TIH_HRD_CALLING 4.3.3 0.0.1
TMB_SNV_INDEL 3.9.15
VARIANT_QC_TO_CSV 3.12.6 1.0.0
VCFTOOLS_TSTV_COUNT 0.1.16
WHATSHAP 2.8
WHATSHAP_TNSEQ 2.8
Workflow v3.5.0-gfdfcf36 25.10.2