Processes

NFCORE_SAREK:UNZIP_ALLELES
1
NFCORE_SAREK:UNZIP_LOCI
1
NFCORE_SAREK:UNZIP_GC
1
NFCORE_SAREK:UNZIP_RT
1
NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_QC_RECAL:SAMTOOLS_STATS
4
CRAM_QC_RECAL:MOSDEPTH
4
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
4
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
4
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
2
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL
2
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
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
4
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
2
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
2
BAM_VARIANT_CALLING_GERMLINE_ALL:GERMLINE_CNV
2
BAM_VARIANT_CALLING_GERMLINE_ALL:BGZIPTABIX_GERMLINE_CNV
2
BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_ESTIMATE_SEX
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:BAM_ESTIMATE_SEX_NORMAL
2
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
2
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT
2
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
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
2
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
2
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
5 1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
2
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso
2
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin
2
BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE
2 2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
2
BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ
1
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ
BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
1
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV
1
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:SOFT_FILTER_VCF
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
2
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
2
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
2
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
1 1
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
BAM_CHIP_DETECTION:TABIX_GERMLINE
HARMONIZE_GERMLINE:BCFTOOLS_NORM
HARMONIZE_GERMLINE:BCFTOOLS_SORT
HARMONIZE_CHIP_PON:BCFTOOLS_NORM
1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT
1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON
BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES
BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER
BAM_CHIP_DETECTION:SENTIEON_GENOTYPE
BAM_CHIP_DETECTION:TRANSFER_CALLER_AD
BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS
VCF_DECONFLICT_VARIANTS:DECONFLICT_VARIANTS
SAREK:GENERATE_CHIP_REPORT
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
10
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
10
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
10
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
10
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
10
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
6 4
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
4
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
1
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
VCF_ANNOTATE_MERGE:TABIX_TABIX
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
1
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
VCF_TMB:TMB
SAREK:AGGREGATE_VARIANT_QC
SAREK:VARIANT_QC_TO_CSV
SAREK:MULTIQC
SAREK:WRITE_TRACKER_YML