Bedtools To Compare A Vcf File From Samtools Mpileup With Dbsnp?

Question

[Deniz]

Hello,

I have one big vcf file which is genereated by samtools mpileup by comparing 6 cell lines to see whether there are SNP differences between them.

I would like to use bedtools for intersecting. How can I do it? do you have some scripts for that.

Thanks

Answer 1

[Swbarnes2]

What's wrong with BEDTools intersectBed? It takes vcf's as inputs.