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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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question about levels of phasing #84

Closed ChristopheLegendre closed 4 years ago

ChristopheLegendre commented 4 years ago

label: question

Hi Dan,

Besides the difference in speed you mentioned in another issue, what are the differences between minimal, conservative, moderate, normal, and aggressive values for the option --phasing-level?

Thanks, Chris

dancooke commented 4 years ago

Hi Chris,

Please see the documentation for the option --lagging-level, which has replaced --phasing-level.

Dan

ChristopheLegendre commented 4 years ago

Hi Dan, Thanks for the quick reply. I will replace --phasing-level with --lagging-level ; Does that mean --phasing-level is going to be deprecated?

dancooke commented 4 years ago

Sorry I should have said "renamed" - I decided to rename it since "phasing"-level was a bit misleading (it doesn't really directly control phasing), plus it makes the relationship with the other haplotype generation options (--extension-level and --backtrack-level) clearer.

ChristopheLegendre commented 4 years ago

Are these options --backtrack-level and --lagging-level available in version 0.6.3-beta? I do not see them when I run octopus/0.6.3-beta/octopus --help or will they be present in the next release onward.

dancooke commented 4 years ago

No - they’re not in v0.6.3-beta. They’re available on the development branch and will be in the next release onwards. There are quiteba few other command line changes coming in the next release - I’ll document them all in the release notes.

ChristopheLegendre commented 4 years ago

Thanks Dan.