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I recently used GATK, the latest version to carry out Indel realignment for my bam files. I have read at few places that one needs to fix the mate position information as the reads mapping position may change during realignment. My question is that does this step is taken care of y GATK automatically or one needs to run Picard fixmates before going for subsequent analysis.

Thanks

There are 5 comments on this article. To see them or add your own, view this post on the forum