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zhengxwen / HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (development version only)
https://hibag.s3.amazonaws.com/index.html
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hg38 hapmap data #29

Open s220224 opened 8 months ago

s220224 commented 8 months ago

In my recent usage of HIBAG, I have hla typed genetic data called from the hg38 reference genome. Though I was able to lifotver the hapmap training data positions, I believe it will be much more accurate if the HapMap_CEU_Geno data were available with the hg38 assembly, especially since this assembly has been out for 10 years. When do you plan to add this data or have it available in the package?

zhengxwen commented 8 months ago

Good suggestion for using hg38 assembly. HapMap_CEU_Geno in the HIBAG package is just an example SNP data file. It is not actually used in the HLA imputation. For real imputation, you should download the platform-specific models.

s220224 commented 8 months ago

Ok, I see. I am trying to run HIBAG on data which was genotyped using Illumina NovaSeq 6000. Can you point me to a model for this platform?