Xiuwen Zheng

Your R version and gdsfmt versions are old. The recent update was made with a focus on R (>= v4.0). I suggest using SeqArray GDS format instead of SNPRelate GDS.

It is quite difficult to answer your question based on your information. If you have detailed SeqArray installation information, it would be helpful. Otherwise, it might be worth considering submitting...

``` hlaBED2Geno(bed.fn, fam.fn, bim.fn, rm.invalid.allele=FALSE, import.chr="xMHC", assembly="auto", verbose=TRUE) ``` Set `import.chr="6"`, try it again.

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,...

Please use platform-specific models

HIBAG does not have allele-level confidence scores, instead it provides sample-level confidence scores. `pred.guess$value$prob` is sample-level score, see `pred.guess$value`.

`pred.guess$value$prob` is sample-level (used to remove low-confidence sample prediction). If you want to remove alleles, consider using the minor allele frequency threshold (e.g., 3 or 5), just like what you...

Sorry, have not checked HIBAG.gpu for a while. Try setting `C_INCLUDE_PATH` (for C header files) or `CPLUS_INCLUDE_PATH` (for C++ header files) environment variables to include `$CUDA_HOME/include`. You might also need...

Not sure what the output of SNP2HLA is. You can use the raw SNP genotypes as the input of HIBAG.

Thanks for the suggestion.