Entering edit mode
2.4 years ago
4galaxy77
2.9k
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?
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.