Comparing and combining vcf files

[gavin.oliver]

Hi,

I am trying to determine if there is an available solution for comparing vcf files and combining them into a single, non-redundant file?

So for example, if I have two vcf files for two patients, I would like to create one unique list of all the mutated locations observed in their genomes. Is there anything else out there or should I just script something?

Thanks in advance.

[aslihan]

you can use samtools mpileup to compare 2 vcf files at the same time.

[swbarnes2]

So you want the union of both files? Try vcftools or BEDTools.

I don't think that mpileup will work with vcf files. What it will allow you to do is to take multiple .bams at once, and make one multi-vcf. But if you don't have the .bams, that won't help much.

[gavin.oliver]

BEDTools appears to be what I am after - cheers!