vcf files generated from intersection/union of multiple callers

Question

[lheisler.bioinformatics]

I'm wondering if anyone is aware of a tool that will perform intersections of calls in vcf files and retain all information in the output. We do look at multiple somatic callers and often want to see which calls are made by both.

The quick solution is to simply filter the results from one of the callers to remove all records not in the other, but it would be nice to retain header information where it differs as well as Info, Filter, and GT differences.

e.g., if each caller generated a separate DP measure, then final output would have to DP values indicated, perhaps DP1 and DP2

Answer 1

[Zev.Kronenberg]

For a strict intersection bedtools works well.

[lheisler.bioinformatics]

Will bedtools generate output in vcf format?

Sorry if I wasn't clear. The need is to generate a new vcf file with the intersection or merge, that includes all info from both source files.