Hello,

I am working on HLA imputation using SNP2HLA. I created the files as below. Output Files

{OUTPUT}.dosage
{OUTPUT}.bgl.phased 
{OUTPUT}[.bed/.bim/.fam/.ped/.map]
{OUTPUT}.bgl.gprobs
{OUTPUT}.bgl.r2

But how can I get the results as below? Do I need to use additional tools? Otherwise the files above do not give us any specific data for allels or amino acids...

1. Classical HLA alleles: HLA_[GENE]_[ALLELE]. 
 2.HLA Amino Acids: AA_[GENE]_[AMINO ACID POSITION]_[GENETIC POSITION]_[ALLELE]. 
 3.HLA intragenic SNPS: SNP_[GENE]_[POSITION]_[ALLELE] 4.Insertions/deletions:[VARIANT]_[GENE]_[POSITION]_[INSERTION/x=DELETION]

Thank you in advance!