MakeReference

MakeReference (v2.0)

(1) Introduction

MakeReference builds a reference panel that can be subsequently used by SNP2HLA for HLA imputation. It is a updated version of the original MakeReference module in SNP2HLA.

(2) Input & output

You would need to files to get started with the panel making:

1. A file (in PLINK format) with all genotyped/sequenced genomic markers (*.bed/bim/fam)
2. HLA alleles (after NomenCleaner) for each individual included in 1 (*.chped)

MakeReference will output

1. the new reference panel in PLINK format (unphased) containing SNPs, HLA alleles, HLA amino acids and HLA intergenic SNPs (*.bed/bim/fam)
2. a combined and phased HLA reference panel for imputing (in vcf format)
3. a maker file (*.markers) with all the markers included in the reference panel
4. a frequency file (*.frq) with all marker frequencies

(3) Usage example

MakeReference 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.

$ python -m MakeReference \
    --variants  MakeReference/example/g1k_subset_snps\ # this is your marker file in the PLINK format
    --chped MakeReference/example/g1k_subset.chped \ # this file includes all HLA types
    --hg 19 \
    --out MakeReference/example/g1k_subset.bglv4 \
    --dict-AA MakeReference/data/hg19/HLA_DICTIONARY_AA.hg19.imgt3320 \
    --dict-SNPS MakeReference/data/hg19/HLA_DICTIONARY_SNPS.hg19.imgt3320 \
    --phasing