read specific region from VCF file to a gwasim type genotype matrix

given region coordinates (locus), the function extracts genotypes for all loci in that region, constructs genotypes matrix G (applies imputation and fixes allele encoding) and computes maf per marker.

read_region_vcf(locus, vcf_file, force_silent = F, GP_map = c(0, 1, 2))

Arguments

locus	region to extract, e.g. 22:17638600-17641201
vcf_file	path to vcf file containing genotypes
force_silent	silence seqminer verbosity (may cause some issues on non-*nix machines)
GP_map	a genotype-phenotype map, by default AA-0, Aa-1 and aa-2

Value

a list with genotypes matrix and maf vector or NULL if region cannot be extracted

Author

Marcin Kierczak <marcin.kierczak@scilifelab.se>