Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses

[Samuel Sosa]

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

[Jean Elbers]

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