function trio_denovo

[fromtotw]

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

[brentp]

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.