Runs
sarek-low-in..0529-033228
Processes
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NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT
968
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT
CRAM_QC_RECAL:SAMTOOLS_STATS
1
967
CRAM_QC_RECAL:MOSDEPTH
87
881
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_ESTIMATE_SEX
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL
206
2
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
179
581
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
499
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
63
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES
VCF_SOMATIC_SNV_INDEL:WHATSHAP
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP
VCF_SOMATIC_SNV_INDEL:TABIX_VEP
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL
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