I am interested in using Octopus to generate candidate variants for varlociraptor. Ideally I would like to skip the haplotyping, genotyping, and filtering steps (which would speed things up a lot) and just get an unfiltered (or very lightly filtered) set of candidates. For this I suggest adding a separate candidate-generation mode, but if you don't want to add that then it would be nice to at least have documented a set of recommended parameter settings. I see that there is a --sites-only option to omit genotype information, but it is not clear whether this skips haplotyping/genotyping/filtering. Thanks!
I am interested in using Octopus to generate candidate variants for varlociraptor. Ideally I would like to skip the haplotyping, genotyping, and filtering steps (which would speed things up a lot) and just get an unfiltered (or very lightly filtered) set of candidates. For this I suggest adding a separate candidate-generation mode, but if you don't want to add that then it would be nice to at least have documented a set of recommended parameter settings. I see that there is a
--sites-onlyoption to omit genotype information, but it is not clear whether this skips haplotyping/genotyping/filtering. Thanks!