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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!
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Per-allele filters?
jamesp
Member ✭
I'm doing analysis on a large multi-ancestry project (XX,XXX exomes) in which approximately 20% of variant sites are multi-allelic. Our sequencing/calling is done at the Broad. It seems that at these multi-allelic sites, only one filter is applied. For example, where there is a SNP and an indel, the SNP may get an indel filter.
Is it possible to disclose how the filter at a given site is chosen? (E.g., by severity, etc.) Is there a plan to allow each variant to have its own filter in the future? (Not sure if there is an internal Broad place to discuss this, since it may have to do more with the pipeline and how SNPs and indel calls are combined than the GATK per se.)
Is it possible to disclose how the filter at a given site is chosen? (E.g., by severity, etc.) Is there a plan to allow each variant to have its own filter in the future? (Not sure if there is an internal Broad place to discuss this, since it may have to do more with the pipeline and how SNPs and indel calls are combined than the GATK per se.)
Answers
Hi @jamesp
Would you please send us the command you are using for variant filtering, the version of gatk and also some records in the vcf where you see this issue.
Once I get this information from you I can bring it up with our dev team.
Here is some info on filtering of germline short variants: https://software.broadinstitute.org/gatk/documentation/article?id=11070
HI @jamesp
I guess I do not quite understand the question here. What is you input data? Were the variants already filtered before you received them? Can you ask the core what pipeline/tools they used?
We haven't heard from you in more than two business days. I will be closing this issue now. But please feel free to ask more questions if reqd.