The Reference VCF Files for HLA Genotyping

[chao]

Hi,

I am trying to genotyping HLA alleles using Platypus.  Where should I download the VCF of known HLA variants?  I searched the IMGT/HLA database (ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/) that supplied by the Nat Genet paper, but I can not find the VCF file for known HLA variants. So should I myself convert the allelelists in the HLA database to VCF format? Or can you supply me a link for the VCF of known HLA alleles that you used when genotyping HLA in the Nat Genet paper?

Many thanks,

Best regards,

Chao 

[Hang PHAN]

Dear Chao,

We did not use a known list of variants for HLA genes to genotype the HLA alleles in the Nat Gen paper. We went around that by aligning the variants called by Platypus to the HLA alleles in the database and compute the maximum likelihood from those alignment. 

However, we are working on an improved version of the pipeline which will be soon available once we are happy with its performance. 

Best regards,

Hang

--
You received this message because you are subscribed to the Google Groups "Platypus Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to platypus-user...@googlegroups.com.
To post to this group, send email to platypu...@googlegroups.com.
Visit this group at http://groups.google.com/group/platypus-users.
To view this discussion on the web, visit https://groups.google.com/d/msgid/platypus-users/43c6a40e-513b-423b-87fd-2d742c427704%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.