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vibansal / HapCUT2

software tools for haplotype assembly from sequence data
BSD 2-Clause "Simplified" License
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Question: support for de novo SNV/INDEL variants #112

Closed jbelyeu closed 3 years ago

jbelyeu commented 3 years ago

Does HapCUT2 phase/haplotype de novo SNVs/INDELs for the proband in a trio? My understanding is that it does not (from skimming manuscript/repo), just trying to make certain. Thanks!

vibansal commented 3 years ago

HapCUT2 phases all heterozygous variants in an individual genome, so it will phase de novo variants in the proband.

jbelyeu commented 3 years ago

Great, thanks (and thanks for the quick response)! How would I go about trio-aware phasing? The goal is to identify the parent of origin for each de novo variant. Or would I need to phase the variants on a per-sample basis and then post-process to see which parent they came from?

vibansal commented 3 years ago

Phasing the child using HapCUT2 should be sufficient. The trio phasing of the genotypes (using Mendelian rules) can be used to determine which haplotype in each block came from the mother or father.

jbelyeu commented 3 years ago

Ok, makes sense. Thanks!