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.
Does the Broad still recommend aligning WXS/WES data to b37/hg19?
According to the article on the the resource bundle (https://software.broadinstitute.org/gatk/download/bundle), you still recommend aligning to b37/hg19 for WXS/WES data (with either hg38 or b37/hg19 for WGS data). However it appears that that recommendation is over 2 years old (the page states that that recommendation is from August 2016).
Do you still recommend using b37/hg19 for WXS/WES data? I'm asking because it appears that a number of the articles on the site assume that one is working with bams that have been aligned to hg38, e.g. this tutorial on using mutect2: https://software.broadinstitute.org/gatk/documentation/article?id=11136