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.
Merging VCF files after HaplotypeCaller->VariantFiltration
I have a RNA dataset that I am calling variants (10 sample). After running gatk4 on all samples independently I want to merge the resulting VCF files for the downstream analysis that requires a multi sample VCF file. I tried to use vcf-merge and bcftools I realize that the INFO field of only one sample is included in the merged file.
How can I merge VCF files without loosing any information about samples ?