Evaluating RMSMappingQuality profile to set threshold
Hello!
I am trying to set a threshold to filter my VCF file by using, among other INFO-annotations, RMSMappingQuality (I am using the GATK best practices workflow).
According to GATK, a reasonable cutoff value for this annotation is >=50, however, given the RMSMappingQuality profile in my data, that leaves out too many SNPs with lower scores than 50(please follow link to figure).
I was wondering what could be a source of the considerable amount of SNPs having low RMSMappingQuality.
Thanks!
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Nicolas Rosewick
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serpalma.v •
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serpalma.v •
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