Picard Fixmate Necessaary · Biostar

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Picard Fixmate Necessaary

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.

picard gatk

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written 13.8 years ago by Ashutosh Pandey

1 answer

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.

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written 13.8 years ago by Ashutosh Pandey

thanks for following up with the answer

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written 13.8 years ago by Istvan Albert

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