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 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 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 TIH_HRD_PLTF 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-g0a8d591 25.10.2