diff --git a/CHANGELOG.md b/CHANGELOG.md index e4dea7c7b9869b3d3abb5a7bdbe41c4eb238aaad..153fa69c72fa136041550e180b2caec3d19da859 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,9 @@ that users understand how the changes affect the new version. version 3.2.0-develop --------------------------- ++ GATK.HaplotypeCaller: Add `--dont-use-soft-clipped-bases` and + `--standard-min-confidence-threshold-for-calling` options. These are + required for RNA seq variant calling according to GATK best practices. + Samtools: Fix quotations in sort command. + Samtools SortByName is now called Sort. + Generalize sort task to now also sort by position, instead of just read name.