Is Picard Fixmate necessary ?
Posted in Ask the GATK team | Last updated on 2012-10-18 01:17:18


Comments (5)

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


Return to top Comment on this article in the forum