How do you carry out Somatic vs Germline mutations analysis when you have vcf files pertaining to only the somatic samples?
Well, then you cannot do a proper analysis right?
You may consider merging your data with 'panel of normal' samples, and proceeding with the analysis in that way. Please take some time to research 'panel of normals':
Just for everybody else, you are referring to this workflow: http://snpeff.sourceforge.net/SnpEff_manual.html#cancer
Kevin
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