We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

MappingQualityRankSumTest and ReadPosRankSumTest

tommycarstensentommycarstensen United KingdomMember ✭✭✭

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?

Answers

Sign In or Register to comment.