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Trio analysis using the GATK toolbox
While I am following the Best Practices documents, I started to get confused about the best sequence of steps to follow, after calling the common VCF file of the child, and parents. Some steps seem not applicable to a total WGS sample of three; like variant-recalibration. Meanwhile, variant recalibration is essential to reduce FPs, and increasing specificity before going any further with analysis.
Although I do understand that tools like PhaseByTransmission, and Genotype Refinement work-flow, are among the most discussed ones, I wonder if there is any "Best Practices" or "Documentation" section that specifically addresses Trio Analysis? Especially with all the additions to the new GATK version.
Thanks in advance for the help.