A subworkflow for calling CNVs using WisecondorX

cnvbambedcramplotsgenomics

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

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

umidedupindexbamsamcram

Included in: nascentriboseqrnaseq

Calculate contamination of the X-chromosome with ANGSD

angsdbamcontaminationdocounts

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

markduplicatesbamsamcram

Included in: atacseqcircdnarnaseq +2 more pipelines

Samtools markduplicate SAM/BAM/CRAM file

markdupbamsamcram

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

Produces comprehensive statistics from BAM file

statisticscountshs_metricswgs_metricsbamsamcram

Subworkflow to run multiple commands in the RSeqC package

rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin

Included in: callingcardsrnaseq

Sort SAM/BAM/CRAM file

sortbamsamcram

Included in: atacseqcircrnacutandrun +9 more pipelines

Split the reads in the input bam by specified genomic region.

splitbamsamcramindex

Produces comprehensive statistics from SAM/BAM/CRAM file

statisticscountsbamsamcram

Included in: atacseqcallingcardscircdna +12 more pipelines