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I read the documentation for MappingQualityRankSumTest and ReadPosRankSumTest: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_MappingQualityRankSumTest.html http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_ReadPosRankSumTest.html
Both pages read: "The ... rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles."
I have quite a few sites for which MQRankSum and ReadPosRankSum are missing. How does VariantRecalibrator handle this missing information?