Runs
feature-sex-..b-0528-1847
Processes
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NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT
6
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT
CRAM_QC_RECAL:SAMTOOLS_STATS
6
CRAM_QC_RECAL:MOSDEPTH
6
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
6
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
6
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
3
BAM_QC_SEX_ESTIMATION:BAM_ESTIMATE_SEX
6
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
15
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC
3
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
3
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
3
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
3
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER
3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION
3
BAM_VARIANT_CALLING_GERMLINE_ALL:GERMLINE_CNV
BAM_VARIANT_CALLING_GERMLINE_ALL:BGZIPTABIX_GERMLINE_CNV
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY
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
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
3
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
3
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
27
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
3
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
3
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
3
BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE
3
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
3
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
3
BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ
3
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ
3
BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS
3
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
3
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
3
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF
3
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
3
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
3
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV
3
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL
3
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT
3
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES
3
VCF_SOMATIC_SNV_INDEL:WHATSHAP
3
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS
3
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP
3
VCF_SOMATIC_SNV_INDEL:TABIX_VEP
3
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS
3
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
3
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
3
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
3
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
3
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
3
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
3
BAM_CHIP_DETECTION:TABIX_GERMLINE
2
HARMONIZE_GERMLINE:BCFTOOLS_NORM
2
HARMONIZE_GERMLINE:BCFTOOLS_SORT
2
HARMONIZE_CHIP_PON:BCFTOOLS_NORM
1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT
1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE
2
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON
2
BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES
2
BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER
2
BAM_CHIP_DETECTION:SENTIEON_GENOTYPE
2
BAM_CHIP_DETECTION:TRANSFER_CALLER_AD
2
BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS
2
VCF_DECONFLICT_VARIANTS:DECONFLICT_VARIANTS
2
SAREK:GENERATE_CHIP_REPORT
2
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
14
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
14
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
14
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
14
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
3
CRAM_HLATYPING_ALL:SEQTK_SAMPLE
3
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
3
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
3
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
14
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
14
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
14
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
14
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
14
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
14
VCF_ANNOTATE_MERGE:TABIX_TABIX
14
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
3
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
3
VCF_TMB:TMB
3
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:VARIANT_QC_TO_CSV
1
SAREK:MULTIQC
1
SAREK:WRITE_TRACKER_YML
1