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Do checks for Mendelian violations via -ped require both parents to be non-missing?
I am interested in checking my VCF for Mendelian violations using the
-ped engine option and the
-mv -invMv options of
To see how it works, I simulated SNP genotypes for a bi-parental cross, and added a few Mendelian violations.
From what I can see, when assessing a given variant, GATK requires both parents to be non-missing, even if some cases of Mendelian violations can be detected when there is only a single parent missing (for instance, when parent1 is "0/0", parent2 is "./." and some offsprings are "1/1").
Can you confirm this behavior? If yes, is there any plan to handle such cases (or should I use PLINK)?