Processes


NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET	1
CRAM_QC_RECAL:SAMTOOLS_STATS		10
CRAM_QC_RECAL:MOSDEPTH	3	7
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
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		5
SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS	5	5	1
SOMATIC_CNV_CALLING:SOMA_CNV_ALLELE_COUNTS	5	5	1
SOMATIC_CNV_CALLING:SOMA_CNV_NORMALIZE	5
SOMATIC_CNV_CALLING:SOMA_CNV_CALL
SOMATIC_CNV_CALLING:SOMA_CNV_EXPORT_VIEWER
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2		5
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
SAREK:AGGREGATE_VARIANT_QC
SAREK:VARIANT_QC_TO_CSV
SAREK:MULTIQC
SAREK:WRITE_TRACKER_YML