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How pgsc_calc handles missing genotype data #307

Answered by smlmbrt
kentaro0209 asked this question in Q&A
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Extract from #305 (comment):

The current pipeline (v2.0.0) in --run_ancestry mode will use the allele frequency in the reference panel to impute the missing allele dosage during PGS Calculation, in the normal mode it will use the allele frequency in your samples to impute the dosage (and also calculate the AVG PGS for non-missing sites).

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@Fiwx
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