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.
The VCF file hava not fully output by using HaplotypeCaller
I have done the SNP and Indel calling about 21 samples by HaplotypeCaller, but I found there have some lines only have part of information in the VCFfile. The informations were cut from the middle of individual ,so I can not fun the filter by this VCF. In the picture ,the line 3094 and 3099 shown this problem, and it is not very commom in this table. Please help me to sovle this problem.