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.
HaplotypeCaller and GenotypeGVCF
I am performing variant calling on Targetted Exome Samples (TES) (Human) using licensed version of GATK (V2014.3-3.2.2-7-g f9cba99)
My samples are amplicon based targetted sequences.
Currently I perform Haplotype calling for individual TES and then Genotype GVCF step for the samples together. My question is :
1) Is it fine to do Haplotype calling and Genotype GVCF steps for all the TES samples together, rather than doing Haplotype calling for individual samples and Genotype GVCF step for the samples together, as mentioned above.