Make input file for NCD1 from VCF

Make input file for NCD1 from VCF

Usage

.vcf_ncd1(x, nind = nind, index.col = index.col, verbose = T)

Arguments

x

An object of class data.table containing typical elements of a vcf file. Output: data.table with columns: CHR, POS, REF, ALT, tx_1 (number of alternate allele copies), tn_1 (total number of alleles) and (if type is ncd2) tx_2 and tn_2

nind

A vector containing the number of diploid individuals from each population to be used. For ncd1, only one population is used.

index.col

First genotype column in VCF file.

verbose

Logical. Printed updates. Default is T.