Hello,

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.

Thanks.