MappingQualityRankSumTest and ReadPosRankSumTest
Posted in Ask the GATK team | Last updated on

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I read the documentation for MappingQualityRankSumTest and ReadPosRankSumTest:

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?

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