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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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Ploidy #91

Open michaeljmetzger opened 4 years ago

michaeljmetzger commented 4 years ago

Is there any chance you know of a way to bring back the ploidy option? I have a tetraploid cancer cell line and I would love to be able to use platypus to call the genotypes (ie. resolve ABBB from AABB, etc). It looks like the ploidy option existed before but it is now depreciated. Is there something that prevents it from working in the current version?

Thanks, Michael

dancooke commented 4 years ago

Platypus is diploid only, which has always been the case as far as I'm aware. You might want to try Octopus - Platypus' successor - that supports non-diploid samples and somatic calling.

michaeljmetzger commented 4 years ago

Thanks! We’ll give it a try.

From: Daniel Cooke notifications@github.com Sent: Tuesday, August 18, 2020 12:35 PM To: andyrimmer/Platypus Platypus@noreply.github.com Cc: Michael Metzger metzgerm@pnri.org; Author author@noreply.github.com Subject: Re: [andyrimmer/Platypus] Ploidy (#91)

Platypus is diploid only, which has always been the case as far as I'm aware. You might want to try Octopushttps://github.com/luntergroup/octopus - Platypus' successor - that supports non-diploid samples and somatic calling.

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