Is Picard Fixmate necessary ?

apandey1

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

Geraldine_VdAuwera

The realigner handles this automatically for you, no need to run fixmates.

apandey1

Thanks a lot.

ralonso

Hello, is then necessary fixmate necessary in any step of the standard gatk protocol?

Regards

ralonso

maybe after markduplicates?

Geraldine_VdAuwera

No, normally you shouldn't need to use fixmates.