A problem on GEMINI de_novo function

[yuanxia...@gmail.com]

When using GEMINI de_novo function, mutations with genotype "0/1, ./., ./." (proband, father, mother) which apparently is a de novo mutation, will be filtered. 

Why this happened?  Can anyone tell me how to solve this problem.

[Aaron Quinlan]

In its default mode, the "de novo” tool requires that both parents have homozygous genotypes, so as to avoid many false positive DNM predictions that can arise when either or both parents have unknown genotypes.

I believe you can explore such cases with the —lenient option.

Aaron

[yuanxia...@gmail.com]

Thank you so much!

在 2018年10月30日星期二 UTC+8上午12:03:28，Aaron Quinlan写道：