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SNP2HLA

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__main__.py
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README.md

SNP2HLA

(1) Introduction

SNP2HLA module (tapa) performs HLA imputation (amino acids, HLA alleles and SNPs) using genotyping data.

(2) Input & output

You would need two things for HLA imputation:

  1. A GWAS dataset contains the MHC region (.bed/bim/fam PLINK format) N.B.: due to the BEAGLE update, unlike SNP2HLA-v1, the correct genomic build (hg19/Grch38) is now important for imputation
  2. Reference dataset (.bgl.phased.vcf.gz/.markers/.FRQ.frq/.bim; output from the MakeReference module)

After imputaton, SNP2HLA will output a single vcf file (*.bgl.phased.vcf.gz).

(2) Usage example

SNP2HLA in HLA-TAPAS has to be implemented in the directory of main project folder. (i.e. 'HLA-TAPAS/' where 'HLA-TAPAS.py' script is.)

$ cd ../ 
# Change your current directory to the HLA-TAPAS main project folder.

$ python3 -m SNP2HLA \
	--target SNP2HLA/example/1958BC \
	--out SNP2HLA/example/IMPUTED.1958BC \
	--reference resources/1000G.bglv4 \
	--nthreads 2 \
	--mem 4g