-
Notifications
You must be signed in to change notification settings - Fork 23
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
function trio_denovo #150
Comments
hi, good questions. Feel free to create your own, more flexible definitions. These are sensible starting points. Indeed they do not find all mendelian violations, they are focused on finding variants that are likely relevant to rare-disease. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
function trio_denovo(kid, dad, mom) {
// alts are 0:hom_ref, 1:het, 2:hom_alt, -1:unknown
if(!(kid.alts == 1 && mom.alts == 0 && dad.alts == 0)){ return false}
// sufficient depth in all
if(kid.DP < 7 || mom.DP < 7 || dad.DP < 7) { return false; }
// no evidence for alternate in the parents
if((mom.AD[1] + dad.AD[1]) > 0) { return false; }
// check the kid's allele balance.
if(kid.AB < 0.2 || kid.AB > 0.8) { return false; }
return true
}
Could you please tell me why here is not checked to see if the kid has a heterozygous genotype (alts == 1) and both parents have a homozygous alt reference genotype (alts == 2)
// 0:hom_ref, 1:het, 2:hom_alt, -1:unknown
function trio_autosomal_recessive(kid, dad, mom) {
return kid.affected && kid.alts == 2 && mom.alts == 1 && dad.alts == 1 && hiqual(kid, dad, mom)
}
The code only assuming 1,1 as recessive (alts = 2) , alts = 0,0 is the dominant
Could you please tell me why here is considering both 0 and 1 could be a dominant
The text was updated successfully, but these errors were encountered: