Processes


NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT
CRAM_QC_RECAL:SAMTOOLS_STATS
CRAM_QC_RECAL:MOSDEPTH
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_CALL
BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE
BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_SCORE
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