GATK licensing moves to direct-through-Broad model -- read about it on the GATK blog

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,
Elise

Tagged:

Best Answer

Answers

  • eflynn90eflynn90 Washington DCPosts: 56Member

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

Sign In or Register to comment.