GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Hello, we've noticed that DP in VCF field FORMAT was missing in our VCFs using Haplotype Caller in GATK version 2.5-2-gf57256b , but it still exists in the header:
I'm commenting here because i found some bug fixes in this release note regarding this issue. Could someone help me check if those problems are back in v2.5 ?
I think what you're referring to (the SomaticIndelDetector bug fix?) was a different issue.
Are you saying that the DP annotation is missing entirely from the vcf produced by the HC, or that the name DP is missing from the format field "legend", while the value is present?