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Test-drive the GATK tools and Best Practices pipelines on Terra
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MappingQualityRankSumTest and ReadPosRankSumTest
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?