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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
No false positives in VQSR tranche plot
I'm doing a large variant calling project on a cohort of ~10,000 exomes. I've run into an issue with VQSR. Everything appears to be working normally except for my output tranche plot (attached), where I'm seeing no false positives. I know this is too good to be true.
From reading other posts on here, I used dbsnp_138.b37.excluding_sites_after_129.vcf , but this didn't change my plots. Some other details : my exomes were generated with different kits. While running VQSR I have tried using -L with the superset of all capture regions ( probably not the best idea) and the intersection of all capture regions (what I intend to use), but the tranche plots look the same regardless.
Using GATK v3.5. Any suggestions would be greatly appreciated.