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Get the ancestral SNP allele knowing the SNP position
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3.0 years ago

I have a big file (461580 rows) containing SNP positions, that looks like this :

1:58989
1:59155
1:59256
1:59260
1:59264
...
X:154396891
X:154396901
X:154397026
X:154397078
X:154427901

I want, as an output, the ancestral allele for each of these SNP.

I tried to work with Allele.bcp that you can find on ftp://ftp.ncbi.nlm.nih.gov/snp/database/shared_data/, as it is advised on the NCBI website (https://www.ncbi.nlm.nih.gov/books/NBK44409/). Unfortunately 1) I have issues to make sense out of this file and all the explanations I found are quite confusing, and 2) in any case it seems that I would need the rsID which I don't have.

I wonder if there is a simple way to get the ancestral SNP allele without knowing the rsIDs.

PS : important precisions, this is human data and I work on with the hg18 build.

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Please if the question is to vague tell me what I should precise.

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