vcfMerger2 is a tool merger for 2 to N somatic variants vcf files.

This tool allows merging from 2 to N somatic vcfs obtained after running different variant callers using the same bam file(s).

vcfMerger2 will generate one vcf.

vcfMerger2 takes RAW VCFs as inputs and outputs a Merged VCF. click here for the RAW VCF Definition

VcfMerger2 has been developped to merge SOMATIC vcfs into one vcf. The current release can merge from 2 to N vcfs.
To see the list variant callers compatible with vcfMerger2 go to "Variant_Callers_compatible" wiki page

Merging GERMLINE vcfs will be available in the next version; some features are already there but are still under development and should be consider as in Alpha version.

See wiki Installation page

The core utility and main purpose of that tool is to MERGE VCFs information into one VCF without losing any data from any of the input vcfs files See QuickStart wiki page.

vcfMerger2 is under MIT licence.