I want to intersect a vcf file with a bed file, that is to get the list of SNPs falling in a specific interval.
For my diploid samples, I could successfully use this command:
vcftools --vcf Sample.1.vcf --bed coordinates.bed --out VCFNEW --recode
But using this for my pooled samples which have a higher ploidy, I get the following error:
Error: Polypolidy found, and not supported by vcftools
I was wondering how I could overcome this problem.