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--phred-scaled-global-read-mismapping-rate query

prasundutta87prasundutta87 EdinburghMember
edited January 2018 in Ask the GATK team

Hi,

I read the description of this parameter in https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php, but it was not clear to me completely, especially the example about 5 mismatches.

Its default value is 45. Does this mean that it won't consider reads which BWA (aligner) asigns MQ (mapping quality) less than 45? Is this switch same as minimum mapping quality in samtools mpileup?

Or its the RMS Mapping quality score in VCF format i.e. MQ?

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