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Indel realignment for MuTect2 in GATK 4.0

srdjansrdjan belgiumMember
edited July 2018 in Ask the GATK team

Hello I have already read that the indel realignment is deprecated in GATK 4.0, as HaplotypeCaller does the realignment, but what about MuTect2?

In one of your posts ( ) I see you already have data where indel realignment was done. Was this intentional?
How do I proceed with the pipeline then?
Should I run indel realignment on my data with 3.8 and then use 4.0 Mutect2?

Best regards,


Best Answer


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