The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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,