which one is paternal or maternal of a genotype? · Biostar

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which one is paternal or maternal of a genotype?

i have compared the genotypes of 1000Genome and GIAB, but the phased data is different. For example, many SNPs in chrX are opposite (eg. chrX:104177984 is 1|0 for GIAB; but 0|1 for 1000G). In the GIAB document(https://docs.google.com/document/d/13XTVwrlAgugYEYtL3W64KX2hy-7xzWNTj8qPN8rULVU/edit), we know that GIAB SNPs are phased in the order paternal|maternal. How about 1000Genome?

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written 6.9 years ago by liying •

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