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.

default read filters in haplotypecaller in GATK


Are these still the read filters applied in GATK haplotypecaller (gvcf mode)?-

• HCMappingQualityFilter (Default 20)
• MalformedReadFilter
• BadCigarFilter
• UnmappedReadFilter
• NotPrimaryAlignmentFilter
• FailsVendorQualityCheckFilter
• DuplicateReadFilter
• MappingQualityUnavailableFilter

I don't remember where I got it from, it must be some old gatk document. But, is it still valid for GATK4?

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