VCF compare: Can anyone suggest an appropriate tool?

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Poornima Nagaraj

SomaticSniper is a tool to find somatic mutation from paired VCFs .

You can also try with Strelka which proves to be more accurate .

The paper which cites that is :http://www.ncbi.nlm.nih.gov/pubmed/22581179

If you have more doubts you can ask the question in this community :

http://seqanswers.com/forums/showthread.php?t=20478