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!
Generating a vcf with the information of specific genome positions (hotspots)
I'm developing a pipeline that needs to take into account the information about variants that are present on a list of hotspots on the genome, because my final analysis uses the information contained on the vcf.
I'm working with WES data, and although I can use as input a bed file with the regions to be analyzed, if the genome region on my hotspot list is showing the same base as the reference genome, it won't appear on my vcf.
So when I filter my vcf for the specific variants on my list, I don't know if the variants that are not present on the file aren't present because it is showing the same base as the reference genome, or because there was a low coverage for the sample on these regions.
I was wondering if GATK best practices pipeline could offer the option to input the list of hotspot so it could generate a vcf with the information for these variants.
If not, what could be the best approach to solve it, and still use GATK's pipeline.
I appreciate the attention,