Processes


NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET	1
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT	56
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT
CRAM_QC_RECAL:SAMTOOLS_STATS	56	9
CRAM_QC_RECAL:MOSDEPTH	56	4
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP	56	3
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM	1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP	56	7
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION	47	1
BAM_QC_SEX_ESTIMATION:BAM_ESTIMATE_SEX	56
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	45	1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE	9	1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON	9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL	9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED	9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC	9
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	9
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	9
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	9
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER	9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION	9
BAM_VARIANT_CALLING_GERMLINE_ALL:GERMLINE_CNV
BAM_VARIANT_CALLING_GERMLINE_ALL:BGZIPTABIX_GERMLINE_CNV
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_FACETS:CONVERT_NORMAL_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_FACETS:CONVERT_TUMOR_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS	47
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	47	2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	47
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	47
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	47
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC	47	5
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	423	3
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	47
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	47
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI	47	2
BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE	47	2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	47
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	47
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV	47
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL	47
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT	47
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES	47
VCF_SOMATIC_SNV_INDEL:WHATSHAP	1143
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS	47
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP	47
VCF_SOMATIC_SNV_INDEL:TABIX_VEP	47
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS	47
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO	47
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF	47
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL	47
BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ	47
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ	1143
BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS	47
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC	47
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING	47
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS	47
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD	47
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2	9
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER	9
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	9
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	9
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM	9
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT	9
BAM_CHIP_DETECTION:TABIX_GERMLINE	9
HARMONIZE_GERMLINE:BCFTOOLS_NORM	9
HARMONIZE_GERMLINE:BCFTOOLS_SORT	9
HARMONIZE_CHIP_PON:BCFTOOLS_NORM	1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT	1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE	9
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON	9
BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES	9
BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER	9
BAM_CHIP_DETECTION:SENTIEON_GENOTYPE	9	3
BAM_CHIP_DETECTION:TRANSFER_CALLER_AD	9
BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS	9
VCF_DECONFLICT_VARIANTS:DECONFLICT_VARIANTS	9
SAREK:GENERATE_CHIP_REPORT	9
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS	197
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT	197
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL	197
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY	197
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA	9
CRAM_HLATYPING_ALL:SEQTK_SAMPLE	9
FASTQ_HLATYPING_OPTITYPE:OPTITYPE	9
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE	9
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	197
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	197
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	197
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	197
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	197
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	197
VCF_ANNOTATE_MERGE:TABIX_TABIX	197
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	47
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	47
VCF_TMB:TMB	47
SAREK:AGGREGATE_VARIANT_QC	1
SAREK:VARIANT_QC_TO_CSV	1
SAREK:MULTIQC	1
SAREK:WRITE_TRACKER_YML	1