Processes


BCL_TO_FASTQ:BCLCONVERT	8
BCL_TO_FASTQ:SAMPLESHEET_CHECK	1
DAQ:FLOWCELL_QC	1
DAQ:CAT_FASTQ	192
FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ	192
FASTQ_NGSCHECKMATE:NGSCHECKMATE_VAFNCM	1
DAQ:ESTIMATEGENDER	192
DAQ:MERGE_GENDER	1
DAQ:FASTP	1536
DAQ:SENTIEON_BWAMEM	1536
DAQ:SAMTOOLS_MERGE	192
DAQ:MARKDUPLICATES_SENTIEON	192
BAM_POSTDEDUP_QC:SAMTOOLS_STATS	192
BAM_POSTDEDUP_QC:MOSDEPTH	192
BAM_POSTDEDUP_QC:SENTIEON_MULTIPLE_METRICS	192
BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS	1536
BAM_POSTDEDUP_QC:SEQTOOL	192
SENTIEON_BQSR:QUALCAL_TABLE	192
SENTIEON_BQSR:QUALCAL_APPLY	192
DAQ:AGGREGATE_POSTDEDUP_QC	1
DAQ:QC_JSON_TO_CSV	1
DAQ:MULTIQC	1
DAQ:WRITE_TRACKER_YML	1
DAQ:GENERATE_RESULTS_CSV	1
GERMLINE_CNV:ClusterPanelRegions	1
GERMLINE_CNV:CalcPanelCoverage	192
GERMLINE_CNV:ProcessBatch	1
GERMLINE_CNV:ModelSingle	2659
GERMLINE_CNV:AggregateBatchPerSampleData	192	1
DAQ:SAMTOOLS_IDXSTATS_COUNT	192
DAQ:WRITE_SKIPPED_CONTROL_METRICS
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	8
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	8
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	72
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	8
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	8
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV	8
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL	8
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT	8
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES	8
VCF_SOMATIC_SNV_INDEL:WHATSHAP	192
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS	8
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP	8
VCF_SOMATIC_SNV_INDEL:TABIX_VEP	8
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS	8
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO	8
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF	8
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL	8
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	8
CONTROL_SOMATIC_VC:MSISENSOR2_MSI	8
CONTROL_SOMATIC_VC:MIMSI_ANALYZE	8
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	20
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC	4
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	4
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	4
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	4
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION	4
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA	4
CRAM_HLATYPING_ALL:SEQTK_SAMPLE	4
FASTQ_HLATYPING_OPTITYPE:OPTITYPE	4
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE	4
CONTROL_GERMLINE_VC:GERMLINE_CNV	4
CONTROL_GERMLINE_VC:BGZIPTABIX_GERMLINE_CNV	4
CONTROL_VARIANT_CALLING:TAR_CONTROL_VC_OUTPUTS	12
POSITIVE_SOMATIC_METRICS:MSI	4
POSITIVE_SOMATIC_METRICS:MIMSI	4
POSITIVE_SOMATIC_METRICS:TMB	4
POSITIVE_SOMATIC_METRICS:POSITIVE_SOMATIC_SNV_INDEL	4
POSITIVE_SOMATIC_METRICS:POSITIVE_SOMATIC_CNV	4
NEGATIVE_SOMATIC_METRICS:MSI	4
NEGATIVE_SOMATIC_METRICS:MIMSI	4
NEGATIVE_SOMATIC_METRICS:TMB	4
NEGATIVE_SOMATIC_METRICS:NEGATIVE_SOMATIC_SNV_INDEL	4
NEGATIVE_SOMATIC_METRICS:NEGATIVE_SOMATIC_CNV	4
GERMLINE_METRICS:GERMLINE_SNV_INDEL	4
GERMLINE_METRICS:GERMLINE_HLA	4
GERMLINE_METRICS:GERMLINE_CNV_METRICS	4
CONTROL_METRICS:MERGE_CONTROL_METRICS	1