Processes

BCL_TO_FASTQ:BCLCONVERT
8
BCL_TO_FASTQ:SAMPLESHEET_CHECK
1
DAQ:FLOWCELL_QC
1
DAQ:CAT_FASTQ
48
FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ
48
FASTQ_NGSCHECKMATE:NGSCHECKMATE_VAFNCM
1
DAQ:ESTIMATEGENDER
48
DAQ:MERGE_GENDER
1
DAQ:FASTP
384
DAQ:SENTIEON_BWAMEM
489 7
DAQ:SAMTOOLS_MERGE
48 1
DAQ:MARKDUPLICATES_SENTIEON
48
BAM_POSTDEDUP_QC:SAMTOOLS_STATS
48 2
BAM_POSTDEDUP_QC:MOSDEPTH
48 3
BAM_POSTDEDUP_QC:SENTIEON_MULTIPLE_METRICS
48
BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS
384
BAM_POSTDEDUP_QC:SEQTOOL
48
SENTIEON_BQSR:QUALCAL_TABLE
48
SENTIEON_BQSR:QUALCAL_APPLY
48
DAQ:AGGREGATE_POSTDEDUP_QC
1
DAQ:QC_JSON_TO_CSV
1
DAQ:MULTIQC
1
DAQ:WRITE_TRACKER_YML
1
DAQ:GENERATE_RESULTS_CSV
1
DAQ:SAMTOOLS_IDXSTATS_COUNT
48
DAQ:WRITE_SKIPPED_CONTROL_METRICS
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
1
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
9
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
1
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV
1
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL
1
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT
1
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES
1
VCF_SOMATIC_SNV_INDEL:WHATSHAP
22 3
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:SOFT_FILTER_VCF
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL
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
1
CONTROL_SOMATIC_VC:MSISENSOR2_MSI
1
CONTROL_SOMATIC_VC:MIMSI_ANALYZE
1
CONTROL_SOMATIC_VC:FILTER_TNSEQ_VCF_FOR_SOMATIC
1
CONTROL_SOMATIC_VC:TIH_HRD_CALLING
1 1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
CRAM_HLATYPING_ALL:SEQTK_SAMPLE
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
CONTROL_VARIANT_CALLING:TAR_CONTROL_VC_OUTPUTS
POSITIVE_SOMATIC_METRICS:MSI
1
POSITIVE_SOMATIC_METRICS:MIMSI
1
POSITIVE_SOMATIC_METRICS:TMB
POSITIVE_SOMATIC_METRICS:POSITIVE_SOMATIC_SNV_INDEL
POSITIVE_SOMATIC_METRICS:POSITIVE_SOMATIC_CNV
1
POSITIVE_SOMATIC_METRICS:HRD
NEGATIVE_SOMATIC_METRICS:MSI
NEGATIVE_SOMATIC_METRICS:MIMSI
NEGATIVE_SOMATIC_METRICS:TMB
NEGATIVE_SOMATIC_METRICS:NEGATIVE_SOMATIC_SNV_INDEL
NEGATIVE_SOMATIC_METRICS:NEGATIVE_SOMATIC_CNV
NEGATIVE_SOMATIC_METRICS:HRD
GERMLINE_METRICS:GERMLINE_SNV_INDEL
GERMLINE_METRICS:GERMLINE_HLA
CONTROL_METRICS:MERGE_CONTROL_METRICS
GERMLINE_CNV:ClusterPanelRegions
GERMLINE_CNV:CalcPanelCoverage
GERMLINE_CNV:ProcessBatch
GERMLINE_CNV:ModelSingle
GERMLINE_CNV:AggregateBatchPerSampleData