Compare different files of SNVs

[Lien]

Dear all,

I used Bowtie and BWA to align my paired-end reads from Illumina Genome Analyzer to the reference genome. I then used Varscan to call variants. However, the SNVs I get, aren't exactly the same.
Does anybody know a way to compare both files with SNVs so that I will get a file with SNVs present in both files and then separate files containing the resultant SNVs?

Thanks a lot!
Lien

[malcook]

looks like varscan will do this itself using the compare subcommand which is documented to "Merge/intersect/substract 2 sets of variants"

never tried it myself