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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!
The text was updated successfully, but these errors were encountered:
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!The text was updated successfully, but these errors were encountered: