I am trying to build a pipeline for detecting de novo mutations for trios WES data. After obtaining the VCF file, and performing all the possible recalibration and refinement steps, I reached this step where I have to phase my variants.
As I have understood, please correct me if the following is wrong:
1- phasing means relating the genotypes to their paternal and maternal origin
2- The de novo mutations will not be phased, because they violate the mendelian law of inheritance
3- PhaseByTransmission can be used to do this job perfectly: i.e. to phase varinats and find denovos
Thanks in advance