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 on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Using dbSNPs for mapping
Hi. So I want to take a dbSNP file and highlight SNPs that are found in some BAM files. Instead of filtering these I want to search for these SNPs only. I will then use these SNP positions as markers to trace recombination events that have occured between some strains I am studying. So far I havn't found a good strategy to accomplish this. I was hoping someone over here knows how to parse the dbSNP, and could guide me through it. Alternatively you could use this idea to generate a new tool! Please let me know if you have thoughts, or questions. Thanks! -Keller