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