feat: Remove PCR duplicates #116
Description
Is your feature request related to a problem? Please describe.
Remove PCR duplicates with a third-party tool.
Describe the solution you'd like
Suggestions from the old discussion
- https://umi-tools.readthedocs.io/en/latest/: @mkatsanto: hard to identify UMIs due to lack of common format; not feasible
- https://sourceforge.net/projects/ngsreadstreatment/: @AngryMaciek tested this extensively, runtime 40h on a paired end sample, rather not suitable for zarp
- samtools-markdup: http://www.htslib.org/doc/samtools-markdup.html (suggestion by @fgypas )
- MarkDuplicates from picard tools: http://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates and https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- (suggestion by @fgypas )(@mkatsanto: this tool would be suitable but works on bam files, which would have to be reverted to FASTQ afterwards to allow other ZARP steps to work)
Additional context
This has been extensively discussed in the old gitlab repository, with no clear conclusion but a trend towards omitting this feature. Saved here mainly for documentation and links in case the discussion reopens.