Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

MappingQualityRankSumTest and ReadPosRankSumTest

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?

Best Answer


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