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Posts by shengchao.li
... I have just successfully imputed chrX on Michigan Imputation Server. You met two separate problems. The first was that your males had heterozygous SNPs. This complaint was from Shapeit. Yes, you have to remove all heterozygous SNPs of males in your data set. I did that by setting those to missing. ...
... A possible reason is that your data is not in GRCh37/hg19 as required by the Michigan Imputation Server. Your data may be in hg18 or hg38. You may want to use tools such as UCSC liftover to modify your data to GRCh37. ...
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