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The 2013 "best practices" workshop slides recommend running PhaseByTransmission followed by ReadBackedPhasing --respectPhaseInput.
The --respectPhaseInput option is not currently listed in the documentation. Does that mean that RBP now always respects phasing in the input VCF?
Does (or did) --respectPhaseInput cause phased sites in the input to be assumed correct, or are they just ignored? That is, does RBP --respectPhaseInput use the partial haplotypes from the input file as evidence?