How to call variants from two samples?

[FrankiB]

Hi,

I'm analyzing two exome deep sequencing libraries, one from cancer cells and the other from normal cells.
I have been through the GATK best practices to end with a recalibrated filtered vcf file (my last step was the Variant Recalibration).

How can I identify genetic variations found between the cancer and normal cells? I'm not interested in variations seen in my samples when
they are compared to the human genome but the differences between my normal and cancer cells.


Any help will be welcome

[GenoMax]

http://www.biostars.org/p/59591/

[FrankiB]

Thank you very much