gatk HaplotypeCaller options

Question

[maricom]

Hi,

I am counting variants using gatk HaplotypeCaller, however, I am not sure the difference between two options, MappingQualityReadFilter and MappingQualityFilter. I read the documents, but still it's not clear to me. Could anybody give me more detailed explanation for them??

MappingQualityReadFilter https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_engine_filters_MappingQualityReadFilter.php#--minimum-mapping-quality

MappingQualityFilter https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_engine_filters_MappingQualityFilter.php

Thank you!

Answer 1

[WouterDeCoster]

Seems like one is from GATK 4, the other from GATK3.8. Take the one that matches with your version of GATK.

Answer 2

[maricom]

Thank you! I'll check which is appropriate for my case.