Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Do checks for Mendelian violations via -ped require both parents to be non-missing?

timflutretimflutre Montpellier, FranceMember

Hello,
I am interested in checking my VCF for Mendelian violations using the -ped engine option and the -mv -invMv options of SelectVariants.
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)?
Best,
Tim

Best Answer

Answers

Sign In or Register to comment.