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PlantandFoodResearch / MCHap

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
MIT License
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Improve defaults for find-snvs #172

Closed timothymillar closed 5 months ago

timothymillar commented 6 months ago

The --ind-maf default setting may not be so good in populations of homozygous samples. Maybe switch out for --maf

timothymillar commented 6 months ago

Actually, this shouldn't be an issue with the way the ind-maf is used: https://github.com/PlantandFoodResearch/MCHap/blob/master/mchap/application/find_snvs.py#L452

need to investigate further.