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.
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.
FilterMutectCalls did not give any records with 'PASS' in the filter field
Hi, I used FilterMutectCalls to filter several VCF files one by one:
java -jar ~/gatk-18.104.22.168/gatk.jar FilterMutectCalls -V original.vcf.gz -O filtered.vcf.gz
And in every output file filtered.vcf.gz, there is no record with 'PASS' in the filter field.
I ran other tools on the same bam files, and they all output variants that passed their corresponding filters.
I use the default parameters when running FilterMutectCalls. It is strange that there are no variants in the filtered.vcf with 'PASS' in the filter field. Can you please help me how to fix it? Thank you!