Picard Fixmate Necessaary

Question

[Ashutosh Pandey]

Hi All, I recently used the latest version of GATK 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 by latest GATK automatically or one needs to run Picard fixmates before going for subsequent analysis.

Answer 1

[Ashutosh Pandey]

Hey Guys,

I got the answer from GATK guys. There is no need to run Picard fix mate as GATK does the required modifications for you.

Thanks.

[Istvan Albert]

thanks for following up with the answer