How can I get the gene position file for hg38 or GRCh38?

[MelanyOuyang]

Dear Author, How can I get a hg38 or GRCh38 version of MHC.hg19.database in order to construct the database for hg38/GRCh38? Thank you in advance.

[adefelicibus]

Hi @AlinaOuyang , I don't know how to construct the MHC database for SOAP-HLA, but you can try two approaches:

• liftover the hg19 regions to hg38;
• this link may help you.

Best,

[MelanyOuyang]

Alexandre, thank you so much for quick reply. I’ve liftovered hg19 to hg38.

发件人: Alexandre Defelicibus @.> 发送时间: 2023年5月15日 21:38 收件人: adefelicibus/soap-hla @.> 抄送: 欧阳丽梅(Limei Ouyang) @.>; Mention @.> 主题: Re: [adefelicibus/soap-hla] How can I get the gene position file for hg38 or GRCh38? (Issue #3)

外部邮件/External Mail

Hi @AlinaOuyanghttps://github.com/AlinaOuyang , I don't know how to construct the MHC database for SOAP-HLA, but you can try two approaches:

• liftoverhttps://genome.ucsc.edu/cgi-bin/hgLiftOver the hg19 regions to hg38;
• this linkhttps://www.ebi.ac.uk/ipd/imgt/hla/help/genomics.html may help you.

Best,

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