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Germline CNV, ploidy and best practices


I'm looking to test the germline CNV tool but I'm having trouble understanding what is the --contig-ploidy-priors file that is needed for DetermineGermlineContigPloidy. Is there a reference I can download or do I have to generate the file somehow? (I'm working on WES samples)
Also, when can we expect the best practices workflow for Germline CNV? It could hold the answer I need.

Many thanks,

Best Answer


  • kimykimy Member
    Ok thank you!
    So this is a default file that can be adjusted, right?
    And I'm guessing that CollectFragmentCounts was renamed CollectReadCounts in the version?
  • AdelaideRAdelaideR Member admin

    Yes, we are about to release a better description of the workflow to follow, so keep your eyes on the board. Thank you for pointing out the name change.

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