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PhaseByTransmission and recombination
I had some questions regarding how PhaseByTransmission interprets recombination events. Does the trio-based phasing explicitly model recombination events?
For two linked loci:
Parent 1: A|T G|A with haplotypes AG and TA
Parent 2: T|T A|A with haplotypes TA and TA
Child 1: A|T A|A with recombinant haplotype AA and normal haplotype TA
Child 2: A|T G|A with haplotypes AG and TA
It is obvious from the data for both possible trios that TA is one haplotype since both loci are homozygous in one of the parents.
Can PhaseByTransmission consider all the offspring at once to identify recombination from AG to AA in parent 1? In other words does it make any sort of haplotypic inference across all the progeny, or does it consider each SNP individually and simply phase that SNP within each trio? The latter case would produce a conflict in the phasing solution for parent 1:
A|T A|G for Child 1 (AA must be on one chromosome and TG on the other)
A|T G|A for Child 2 (AG must be on the same chromosome because parent 2 is homozygous at both loci)
Please let me know.