Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
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!
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.
Filtering variants after calling on intervals - VQSR vs Hard-filter vs CNN
MehulS
Member ✭
Hi. I have ~80-100 low-coverage (5-10X) WGS samples which I want to run through a joint genotyping (GVCF) workflow. I have "Halotype-called" (ERC GVCF) variants on my genes of interest using an interval list (contains 90 genes).
Will VQSR work with the final interval-subsetted VCF ? If no, would it help if I extended my intervals to cover a 100 more genes and extend the intervals further ? I'm very reluctant to call variants on the whole genome samples since I'm in a hurry and HaplotypeCaller takes too long (~6 hours).
PS I have one high coverage sample which I can download but would prefer not to.
Apart from that I have previously made calls on the same samples (but over the whole genome) by which I plan to use in my training set.
Answers
HI @MehulS
I don't see why not
Thank you for your reply @bhanuGandham . I am concerned because VQSR needs a lot of variants to build a model while my resulting raw variants will be restricted to my intervals which I have called the variants on. Is there any specific threshold for the minimum amount of variants VQSR needs to build a good model, or at least work ?
Update: I did a round of genotype GVCFs on 85 samples and got 12180423 variants. Is this good enough for VQSR to at least work ?
@MehulS
yes that should work.