Open changebio opened 2 years ago
paramlink2 can handle the halftyped issue
How does it handle this?
One solution is to set all halftypeds to missing genotypes (0/0). @gaow
Looks like the easiest thing to do, but could you double check with Jurg?
Okay. I will double check with Jurg.
I don't know how exactly paramlink2 does. Based on my understanding, we can calculate the likelihood of a variant only if there are no mendelian errors. I think pseudomarker must set rules to filter markers with halftyped in some reasons.
I don't know how exactly paramlink2 does.
Can you investigate?
Pedigree 1007 Person 1007_40 halftyped (1/0)
The halftyped came from phasing haplotypes. In some case, only one Haplotype is phased. paramlink2 can handle the halftyped issue. However, pseudomarker will report an error. One solution is to set all halftypeds to missing genotypes (0/0). @gaow