I am interested in finding copy number variation in my samples. I have looked for SNPS and INDELS with GATK UnifiedGenoTyper (still have to use it with haplotypecaller). Is there a walker to find CNV's (duplications or deletions) in GATK?
Hope to hear from you soon.
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.