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A subworkflow for calling CNVs using WisecondorX

cnvbambedcramplotsgenomics

Includes: wisecondorx/convertwisecondorx/predict

Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.

gatk4mutect2genomicsdbimportcreatesomaticpanelofnormalsvariant_callinggenomicsdb_workspacepanel_of_normals

Included in: createpanelrefs
Includes: gatk4/mutect2gatk4/genomicsdbimportgatk4/createsomaticpanelofnormals

umicollapse, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram

Included in: rnaseq
Includes: umicollapsesamtools/indexsamtools/statssamtools/idxstatssamtools/flagstatbam_stats_samtools

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram

Included in: nascentriboseqrnaseq
Includes: umitools/dedupsamtools/indexsamtools/statssamtools/idxstatssamtools/flagstatbam_stats_samtools

BAM deduplication with UMI processing for both genome and transcriptome alignments

deduplicationUMIBAMgenometranscriptomeumicollapseumitools

Included in: rnaseq
Includes: umitools/prepareforrsemsamtools/sortbam_dedup_stats_samtools_umicollapsebam_dedup_stats_samtools_umitoolsbam_sort_stats_samtools

Calculate contamination of the X-chromosome with ANGSD

angsdbamcontaminationdocounts

Includes: angsd/docountsangsd/contamination

Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats

markduplicatesbamsamcram

Included in: atacseqchipseqcircdna +3 more pipelines
Includes: picard/markduplicatessamtools/indexsamtools/statssamtools/idxstatssamtools/flagstatbam_stats_samtools

Samtools markduplicate SAM/BAM/CRAM file

markdupbamsamcram

Includes: samtools/collatesamtools/fixmatesamtools/sortsamtools/markdup

Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.

ngscheckmateqcbamsnp

Included in: sarek
Includes: bcftools/mpileupngscheckmate/ncm

Produces comprehensive statistics from BAM file

statisticscountshs_metricswgs_metricsbamsamcram

Includes: picard/collectmultiplemetricspicard/collectwgsmetricspicard/collecthsmetrics

Subworkflow to run multiple commands in the RSeqC package

rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin

Included in: callingcardsrnaseq
Includes: rseqcrseqc/tinrseqc/readduplicationrseqc/readdistributionrseqc/junctionsaturationrseqc/junctionannotationrseqc/innerdistancerseqc/inferexperimentrseqc/bamstat