If you're a developer who uses the GATK framework, you may have noticed that the 3.2 release broke existing third-party walkers. This happened because we had to do some codebase-wide refactoring/renaming that changes package names and classpaths (most obviously, renaming all instances of "sting" to "gatk"). We're sorry for the inconvenience but this was necessary as a preparation step on the road to providing GATK as a maven artifact.
We have posted a document that details the changes and explains how to update third-party code to work with GATK framework versions 3.2 onward here.
While we're on this topic, it seems that the IntelliJ set up instructions are a little outdated (in part due to the renaming), so we'll be updating that as well in the near future.
Following GATK's best practices, I have individually realigned/recalibrated my sample-lane bams and merged them by sample:
sample1_lane1.dedup.realn.recal.bam --> sample1_lane2.dedup.realn.recal.bam --> sample1.merged.bam sample2_lane1.dedup.realn.recal.bam --> sample2_lane2.dedup.realn.recal.bam --> sample2.merged.bam ...
I am ready to dedup and realign my sample merged bams, however I am uncertain on the best approach. Is the consensus to convert back to fastq via Picard (MarkDuplicates, SortSam, and SamToFastq) and then run bwa mem? Or is it more expedient/accurate to realign the sample-merged bam using bwa aln followed by bwa sampe?