The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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)?