GATK tooling update to fix Bug in Markduplicates #1880
Description
Related to this, it seems that there has been a bug in Picard MarkDuplicates related to read groups (broadinstitute/picard#1936, broadinstitute/picard#1937). Apparently, read group information has not been used, and everything has just ended up in the same read group "RG." So, in order to use read group information, one needs to update Picard to 3.2.0+ (included in gatk4 v4.6.0.0).
Originally posted by @pontushojer in #1715