GATK best practices for exome/targeted capture (small region)

nitinCelmatixnitinCelmatix NYCMember
edited January 2016 in Ask the GATK team

I was wondering if there is a set of best practices developed specifically for calling variants from a small region target capture sample. I looked but I could not find a one-stop comprehensive documentation. If not, are there some specific recommendations (such as certain values of parameters for the exome/targetome analysis? For eg., -L.


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