If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Should I run CombineVariants on indels and snps after VQSR/hard filtering?

Before VQSR/hard filtering, I have one single vcf file.

According to the best practice doc, I need to split it into indels and snps and run VQSR/hard filtering.

At the end, I have one filtered vcf for indels and one filtered vcf for snps.

I wanted to get one single vcf back, so I tried CombineVariants. However, I am getting two samples in the combined vcf if I run it with UNIQUIFY. I can get a vcf with only one sample using PRIORITIZE with snp over indel. Is PRIORITIZE the right way to merge?

Best Practice doc doesn't seem to mention whether to run CombineVariants after filtering. Is CombineVariants possible or desirable? If it is not desirable, does that mean downstream analysis like VariantEval should run separately for snp and indel???

Thanks a lot in advance


Sign In or Register to comment.