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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).
Now I would like to keep the variants (variations) found between normal and cancer cells and keep only those which have been retained according to plots produced during the previous step i.e VQSR.
I'm not sure which parameters I should select in my command line in order to achieve my goal.
I have searched through the documentation on your website, but still not sure...
Any help will be welcome