If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Outlook on Grch38/hg38 for in exome and other targeted sequencing
Dear GATK team,
First of all, congratulations on releasing GATK4!
I was wondering, on this page: https://software.broadinstitute.org/gatk/download/bundle it is mentioned that the human genome reference builds you support actively are the following:
For Best Practices short variant discovery in exome and other targeted sequencing: b37/hg19
Last year we build an RNAseq pipeline and a preliminary DNAseq pipeline around GRCh38. Can you perhaps indicate how far out the publication of Best Practices for short variant discovery in exome and other targeted sequencing using GRCh38 is?
By the way, the link below the bullet points (https://software.broadinstitute.org/gatk/user%20guide/article.php?id=1213) gives a 404.
Keep up the good work,