R script to convert VCF format biallelic SNP data to the format required for the conStruct R package (https://github.com/gbradburd/conStruct)
Requires the following packages: vcfR, fields, dplyr, argparser
run install.packages('vcfR', 'fields', 'dplyr', 'argparser')
usage example: Rscript vcf2conStruct.R --vcf my_file.vcf.gz --metadatafile my_meta.txt --outname my_conStruct
OR: Rscript vcf2conStruct.R -v my_file.vcf.gz -m my_meta.txt -o my_conStruct
In the above example, the output will be saved as my_conStruct.RData. The object name will always be conStruct_object (after loading into R using load("my_conStruct.RData").
Requires a metadata file with no header with columns in this order: 'sample population longitude latitude' (can be tab or space delimited)