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AlexTISYoung / snipar

Imputation of parental genotypes, inference of sibling IBD segments, family based GWAS, and polygenic score analyses.
MIT License
24 stars 5 forks source link

negative imputed genotype #8

Closed yystat closed 4 years ago

yystat commented 4 years ago

Hello,

Curiously I just found that a few SNP's imputed genotype is negative! Most of them are -1, some -0.5. Is this possible? I'm using parent-offsprings data. (Full sibling data seems to be fine.) Any suggestions how should I treat them? Recode them to NA? Thanks!

Josh

MoeenNehzati commented 4 years ago

Hi, My guess is they are negative since the IBD inference for those SNPs is incorrectly state 0. I think replacing them with some form of NaN value is the best course of action. I'll fix the package to convert these negative values to NaN before returning them. Best, Moeen

yystat commented 4 years ago

Got it, thanks!