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1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
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Selection of variants when comparing two libraries

frankibfrankib Sherbrooke, CanadaMember Posts: 41

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).

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

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