MarkDuplicates documentation

[adthrasher]

Apologies if this is the wrong place, but I can't find a repository corresponding to the documentation available at: https://gatk.broadinstitute.org/hc/en-us/articles/30332022936475-MarkDuplicates-Picard.

There are a few issues with that page. First, sorting is described differently depending on where you are. The main documentation states, "The program can take either coordinate-sorted or query-sorted inputs, however the behavior is slightly different.". However, the documentation for the INPUT parameter states, "One or more input SAM, BAM or CRAM files to analyze. Must be coordinate sorted.".

In addition to that, the documentation does not describe the tool's ability to merge input files. This is used in some of the public facing Broad WARP pipelines, but isn't documented for users. Does that merge work on either type of sorting or does it require coordinate-sorted (or just collated) input files?

[kockan]

I'm pretty sure that the main documentation is correct, MarkDuplicates should work for both coordinate-sorted and query-sorted inputs.

Do you have links to any of the WARP pipelines you've mentioned?

[adthrasher]

Sure, here is one example where multiple INPUT= arguments can be used to pass multiple BAMs to MarkDuplicates.