Prepare the phased genotype into the standard format

This function used to prepare phased genotype file to standard format in 'HandyCNV' to get haplotype for any interested genomic region, The input file should phased by Beagle 5.1.

prep_phased(phased_geno, convert_letter = FALSE)

Arguments

phased_geno	phased genotype file from Beagle 5.1, the first nine columns contain basic information, the rest are genotype
convert_letter	convert allele from 0, 1 to letter in REF and ALF

Value

A list contain map and genotype information