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Does HaplotypeCaller use a MAPQ cut-off?

eflynn90eflynn90 Washington DCPosts: 56Member

I thought I had seen something in the HaplotypeCaller documentation that said HC didn't look at reads with MAPQs less than 30 by default, and I thought there was a parameter to change this. Was this an older version of HC, or am I just making that up? Does HC use a MAPQ cut-off for reads contributing to the variant call?

Thank you,


Best Answer


  • eflynn90eflynn90 Washington DCPosts: 56Member

    Ahh, thank you!! I knew I had seen it somewhere.

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