Problems with shapeit output

odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool

MIT License

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Problems with shapeit output #34

Closed duzc-Repos closed 3 years ago

duzc-Repos commented 3 years ago

Hi, Prof. I wonder how the shapeit deal with missing data. More specifically, if a snp is coded as "0 0 0" in gens format, what it will be output in haps format? Will it be discarded or any other situation?