Evaluating RMSMappingQuality profile to set threshold
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16 months ago
serpalma.v ▴ 70

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).

enter image description here

I was wondering what could be a source of the considerable amount of SNPs having low RMSMappingQuality.

Thanks!

SNP snp gatk variant calling filtering • 289 views
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