Question: Genotype QC for training

zhengxwen / HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (development version only)

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Question: Genotype QC for training #14

Closed adiamb closed 1 year ago

adiamb commented 3 years ago

Since many snps in the HLA region typically don't obey the HWE, do you recommend not applying a HWE filter for quality control steps before doing the training? can you advice please? thank you

zhengxwen commented 3 years ago

No need to use HWE filter in QC, the HIBAG algorithm is robust to the departure of HWE.