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 November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
How can I specify unmmaped regions with FastaAlternateReferenceMaker
I have a set of high-quality SNPs that were jointly called off a merged, realigned BAM. I then created a VCF for each sample using SelectVariants, re-ran UnifiedGenotyper with EMIT_ALL_SITES, and thinned the resulting VCF to no-call sites so I could mask them. Next, I produced a FASTA file for each sample with Ns at no-call sites and SNPs in their appropriate positions with FastaAlternateReferenceMaker. How can I use GATK to specify contigs where no reads were supported for a given sample and use this information to avoid outputting these regions via the -L flag with FastaAlternateReferenceMaker? Apologies if this is trivial, but I haven't found a clear solution.