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tatsuhikonaito / DEEP-HLA

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Obtain the imputed SNP VCF #10

Open troyeeee opened 1 year ago

troyeeee commented 1 year ago

Hello,

I have used DEEP-HLA for HLA imputation, and I noticed that the current output only includes the HLA typing results. I am interested in obtaining the imputed SNP VCF file after the imputation process. Could you please guide me on how to generate or obtain the imputed SNP VCF file using DEEP-HLA?

I appreciate your help. Thank you in advance!

Best regards, Troye

tatsuhikonaito commented 1 year ago

Hi Troye,

Thank you for getting interested in using DeepHLA for imputing SNPs in VCF files. Actually, DeepHLA was made specifically for imputing HLA alleles. You may be able to use it for SNP imputation by listing all SNPs to impute in an HLA info json file; however, it is not a recommended way. There are some other tools for SNP imputation based on deep learning, which may meet your purpose.

Best regards, Tatsuhiko