Hi GATK team,
I recently downloaded GATK2.2.5 and re-analyzed a small part of my data which was analyzed by2.1.8 pipeline previously, following the same parameters. However I found the new pipeline identified 7247 variants (Q30) while 2.1.8 previously detected 5119. Fortunately, 5118 of the previous ones were recovered by 2.2.5 and 4845 of them were given the same genotypes for all samples. But I still want to know whether the previous version would indeed miss some data.
I checked your release notes, but it just claimed some performance issues from 2.1.* to 2.2.* for HC.