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Created 2014-09-29 18:10:44 | Updated 2014-09-29 18:14:33 | Tags: developer third-party-tools sting
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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While we're on this topic, it seems that the IntelliJ set up instructions are a little outdated (in part due to the renaming), so we'll be updating that as well in the near future.

Created 2015-05-09 14:48:21 | Updated | Tags: best-practices bam third-party-tools picard
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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?