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# Is Picard Fixmate necessary ?

Member
edited October 2012

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

Post edited by Geraldine_VdAuwera on
Tagged:

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

• Member

Thanks a lot.

• Member

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

Regards

• Member

maybe after markduplicates?