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?
m struggeling with some statistics given by the vcf file: the Ranksumtests. I started googleing arround, but that turned out to be not helpfult for understanding it (in may case). I really have no idea how to interprete the vcf-statistic-values comming from ranksumtest. I have no clue whether a negative, positive or value near zero is good/bad. Therefore im asking for some help here. Maybe someone knows a good tutorial-page or can give me a hint to better understand the values of MQRankSum, ReadPosRankSum and BaseQRankSum. I have the same problem with the FisherStrand statistics. Many, many thanks in advance.
I have run UnifiedGenotyper with the -glm options SNP and BOTH. These two approaches yield identical variants and identical genotype likelihoods (at least the first 100k variants I checked). However, a few of the annotations have different values: BaseQRankSum MQRankSum ReadPosRankSum
-glm SNP on the left and -glm BOTH on the right:
Why is that?
I noticed another user got different variants, but I get the same variants and the same likelihoods: [http://gatkforums.broadinstitute.org/discussion/1782/unifiedgenotyper-different-glm-value-result-in-different-sets-of-variants]
I ran single threaded.
I use MQRankSum and ReadPosRankSum for VariantRecalibrator, so it affects my downstream results, if the annotations are -glm dependent. Hence I am asking my question. I hope you can illuminate me. Thank you.