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CNV length - by genome, by region

redzengenoistredzengenoist Member
edited April 2013 in Ask the GATK team

Hello Geraldine et al,

I've a question about CNV calling, which you might or might have an answer for. We're doing a case/control analysis on two cohorts, and one of the analyses we'd like to carry out is an examination of CNV length - one thing we want to do is analyse by genome (average site above/below average, say), and by region (same general idea).

While calling SNPs and indels seems straightforward enough with UG, I wonder if you have a best practice for calling CNV - or rather, a candidate for what might become an integrated best practice? Maybe I can even help with maturation/integration.

Thanks for your relentless work on the site, tools and community, this is the place to be.

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  • redzengenoistredzengenoist Member
    edited April 2013

    I should have added one more important piece of information:

    I am right now experimenting with XHMM. I am not yet sure whether it is the way to go, since it's a tool for highly covered target regions, while our data is low coverage WGS. We'd optimally like to do a very large number of regions, though a handful of target regions would be acceptable.

  • I'll do that, thanks Geraldine.

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