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How does PhaseByTransmission define the phasing of Father and Mother?
Hi, I have genotyped a trio, and then phased them using PhaseByTransmission of GATK Tools. I have then parsed the output vcf file using BCFTools query command. The output file looks like as follows:
CHR POS FAT MOT CHILD
20 65288 G/T ./. ./.
20 65900 A|A A|G A|A
20 66720 ./. C/A C/A
20 68749 T|C C|C C|T
20 69094 G/A ./. ./.
The phasing information can be interpreted as Mother|Father. Now, I understand that the Child Phasing can be done by applying Mendelian Laws. But How the phasing of Father or Mother is done here? For example here "20 68749 T|C C|C C|T", every person of the trio is phased; even the father (het) without even knowing grand parents of the child. As I am a new researcher in this field, your clarification will help me a lot to understand phasing.
Thank you very much,