If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
VQSR failed with "No data found" with whole genome variant calls, but succeeded with filtered set
I ran VQSR on the SNP calls from a WGS sample mapped to b37+decoy reference, it failed at the training step with error message "No data found". I then removed the SNP calls on the small contigs (unmapped/random/decoy) and only retain the ones mapped to the major chromosomes, and passed this new set to VQSR training with the same parameters again. It was successful.
From what I understood (but I may be misunderstanding) from the VQSR documentation, the gaussian mixture model construction should not rely on chromosomal locations, but only the variant annotations. If the whole genome job failed with "no data found", either no enough bad variants or good variants, I'm wondering how could it then find enough data with the filtered set?
For comparison I ran VQSR for another WGS sample which succeeds on the training both unfiltered or filtered. It seems the FILTER column in the final results will have lots of differences between filtered and unfiltered, which can be expected because the variants pool has been changed. But I'm also wondering are both results OK to use for downstream analysis?
Thank you very much for providing any information/comment.