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detail information for --minimum-mapping-quality option in HaplotypeCaller

maricommaricom Member
edited July 2019 in Ask the GATK team

I posted the same question by adding the comment to a different post, but I couldn't get the answer yet, so let me post the same one here.

I'm using HaplotypeCaller to find variants, however, could you tell me about the --minimum-mapping-quality option?
If I set this option, what kind of calculation does GATK do??
I read a page where there is an explanation of the meaning of the option, but I can't tell what kind of reads will be eliminated after I apply this option.

Thank you in advance!
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