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luntergroup / octopus

Bayesian haplotype-based mutation calling
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Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses #272

Open bosamu05 opened 8 months ago

bosamu05 commented 8 months ago

Hello everyone.

It could be a silly question. What position are maternal and paternal haplotypes in phased genotypes in Octopus? I just want to confirm if the first position (left) of phased genotypes always indicates the maternal haplotype and the second position (right) indicates the paternal haplotype.

I mean if the genotype is 1|0, then, 1 comes from the maternal haplotype and 0 comes from the paternal haplotype? Information provided from TRIO analyses.

Genotype - Maternal Haplo - Paternal Haplo 1|0 - 1 - 0 0|1 - 0 - 1 1|2 - 1 - 2 0|1 - 0 - 1 2|0 - 2 - 0

Thank you in advance

jelber2 commented 8 months ago

Without going through the code extensively, https://github.com/luntergroup/octopus/blob/develop/src/core/callers/trio_caller.cpp trio_caller.cpp extensively has the pattern of maternal, paternal, child, so that would be my guess