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.
Genotypes and VariantsToTable walker
I just started using VariantsToTable tool, which works great. I am still facing a problem with genotype fields extracted from vcf as the numbered genotypes (0/1) are changed to nucleotides (T/C). That is something that I do not want. Therefore, I would like to ask, if there is a way to stop this happening, so that the walker leaves genotypes to number format as they are in vcf file?