How To Deal With The Duplicate Snp Location In Hapmap Or 1000G Genotypes Files?

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11.5 years ago

J.F.Jiang ▴ 930

Hi all,

I am processing the genotypes of HapMap individuals, however, it seems that a genotypes file will always carry some SNPs with duplicate but different genomic locations.

So how to deal with such a thing?

And same thing is the Common SNPs genomic location file from UCSC database, seems some SNPs have more than one genomic locations in the file. And of course, one description might be wrong, so is there any link/file that can eliminate such a problem?

Thanks

snp hapmap 1000genomes genotype • 2.7k views

ADD COMMENT • link 11.5 years ago by J.F.Jiang ▴ 930

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This may help

ADD REPLY • link 11.5 years ago by seth hearld ▴ 30

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thanks, but it did not offer any direct solution to get the file with unique positions

ADD REPLY • link 11.5 years ago by J.F.Jiang ▴ 930

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Hi, Could you find the solution? I tried to merge my cases with 1000G reference panel(b37-phase 3) and have the same problem with that. How you dealt with the duplicate snps or multiple positions?

ADD REPLY • link 8.2 years ago by fatima ▴ 20

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