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.
Order of the sample names in cohort VCF file using GenotypeGVCFs
I wanted to produce the cohort vcf file from several g.vcf files made using HaplotypeCaller. I used the 'GenotypeGVCFs' and gave a list of g.vcf files. The order of samples in the final vcf file is different from the gvcf file list I provided. It looks like it sorted alphabetically with the sample name. How can I get samples in the same order as in the gvcf file list? I am using GATK 3.3.