A subworkflow for filtering differential abundance results

Extract archive(s) from any format Currently supported format are .gz, .tar.gz, .zip

Includes: gunzipuntarunzip

A subworkflow for calling CNVs using WisecondorX

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.

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

Includes: umicollapsesamtools/indexsamtools/stats and 3 more modules

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

Includes: umitools/dedupsamtools/indexsamtools/stats and 3 more modules

BAM deduplication with UMI processing for both genome and transcriptome alignments

Calculate contamination of the X-chromosome with ANGSD

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

Samtools markduplicate SAM/BAM/CRAM file

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