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!
information about GATK "Filter" field
I'm analyzing the vcf files obtained by applying your GATK variant calling tool. I'm new in this kind of analysis, and I would like to kindly ask you some additional information about the filtering step of the VCF file according to the "FIlter" field. In details, I read that variants that are above the defined FILTER VQSLOD threshold , pass the filter, so the FILTER field will contain PASS, while variants that are below the threshold will be filtered out; however, they are written to the output file, but in the filter field they have the name of the tranche they belonged to. I also read about the tranches, corresponding to different levels of sensitivity and accuracy of the variants. In my VCF file, I have 4 groups of variants according to the "Filter" field:
I can't fully understand the meaning of the tranches, and the probability of false positives for each one. I would like to kindly ask you how I can interpret the three categories defined as "VQSRTranche", and if you suggest to remove or not these variants for subsequent analyses, and consider only the "PASS" filter.
Thank you in advance for your time and kind attention.