I am trying to study individual chromosomes in my dataset, and create a plink file in vcftools with a single chromosome. However the chromosomes are labeled as Pseudochromosome_1, 2, 3, etc. Thus, when I enter the command:
vcftools --vcf filename.vcf --plink --chr 1 --out filename
I don't know what to enter for "chr" - 1, 2, 3, etc does not work.
Thanks for your help!