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.
COSMIC and dbSNP files for MuTect
I'm having trouble finding the recommended COSMIC and dbSNP file for hg19 to use with MuTect (hg19_cosmic_v54_120711.vcf and dbsnp_132_b37.leftAligned.vcf). I can't find these in any of the bundles on the GATK public FTP site. I see a dbSNP file called dbsnp_132_b37.vcf; is this the same? I don't see any COSMIC file at all. I'm currently using bundle 2.3 for hg19 for the dbSNP files (and the standard indels from 1000G and Mills for indel realignment). Thanks!