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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
I have problem with Hard Filtering, anyone to help?
Hi guys, I was trying to run the below command and I got an invalid error from my argument. I could not find any mistake in my command and have also regenerated my input raw SNPs file but error remain the same. I could not also find any thread that have addressed this problem. What do you think I am doing wrong? logfile=filtered.error gatk 3.7.0 \ -T VariantFiltration \ -R fasta.fa \ -V raw_SNPs.vcf.gz \ --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" \ --filterName "default_SNP_filter" \ -o filtered_SNPs.vcf \ 2> >(tee "$logfile")
ERROR Invalid argument value '2.0' at position 9. ERROR Invalid argument value '||' at position 10. ERROR Invalid argument value 'FS' at position 11. ERROR Invalid argument value '>' at position 12. ERROR Invalid argument value '60.0' at position 13. ERROR Invalid argument value '||' at position 14. etc..