Converting RSIDs in the HLA region (e.g.) HLA-A*:01:01g-B*08:01 format?
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7 weeks ago
4galaxy77 2.3k

I imputed HLA genotypes using the Michigan Imputation Server, resulting in a vcf which looks like this:

6       28000361        rs1529749       T       C       .       PASS    .
6       28000610        rs17765491      C       A       .       PASS    .
6       28001003        rs17708949      A       C       .       PASS    .
6       28001033        rs149941        T       C       .       PASS    .
6       28001610        rs149942        T       C       .       PASS    .
6       28002045        rs9393873       G       A       .       PASS    .
6       28002139        rs77234126      G       A       .       PASS    .
6       28002388        rs149943        G       A       .       PASS    .
6       28002818        rs149944        C       T       .       PASS    .
6       28002853        rs149945        T       C       .       PASS    .

I'm interested in converting/annotating the vcf so that the the allele coding is in the format of e.g. HLA-A*:01:01g-B*08:01.

I've googled around a lot, but can't find anything. Does anyone know how I can achieve this?

SNP HLA rsid • 183 views
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Entering edit mode

Perhaps it may be possible to go the other way? Just speculating. Download all ID's in format you need and then map them back onto the list you have.

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