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.
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!

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.

Can FilterMutectCalls filter by coverage?

JulsJuls Member ✭✭

Dear GATK team,

I could like to filter my mutect2 vcf file by coverage as well and thereby exclude high and low coverage regions like it is possible with VariantFiltration:

gatk VariantFiltration -R ref.fasta -V variants.vcf --filter-expression "!vc.hasAttribute('DP')" --filter-name "noCov" --filter-expression "vc.hasAttribute('DP') && DP < cutoffLow" --filter-name "lowCov" --filter-expression "vc.hasAttribute('DP') && DP > cutoffHigh" --filter-name "highCov" -O variants_filtered.vcf

Is this possible with FilterMutectCalls or can I use VariantFiltration on a mutect2 file as suggested above in addition to the regular filtering with FilterMutectCalls ?

Thank you so much!

Best Answer

  • bhanuGandhambhanuGandham Cambridge MA admin
    Accepted Answer

    Hi @Juls

    If you specifically want to filter for coverage then yes feel free to experiment with VariantFiltration. FilterMutectCalls does a lot of modeling and machine learning under the hood. If you absolutely must do coverage filtering, sure, use VariantFltration, but there's almost never a good reason not to rely solely on FilterMutectCalls. VariantFiltration can only do ad hoc hard filters.

Answers

Sign In or Register to comment.