SubcloneSeeker SNP import from flat file
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8.1 years ago
hxrts • 0

I'm having some trouble parsing the documentation for SubcloneSeeker. The "Sqlite based object archiving" section on the utils page mentions importing flat VCF files, and the class hierarchy pages indicate that SubcloneSeeker can make inferences using SNP data (as opposed to cluster information). The flat file-to-database conversion documentation makes no mention of this step - am I misinterpreting the documentation somehow?

VCF SNP IO clonality • 1.6k views
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I haven't used SubcloneSeeker in a while, partially because running it is a pain. I find that clonevol is much easier to use and provides comparable (and possibly even superior) results. https://github.com/hdng/clonevol

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Thank you for your reply. SubcloneSeeker is indeed obnoxious to use. I'm vetting several algorithms and will give clonevol a try as well. If anyone does happen to have information on how to properly implement SubcloneSeeker I'd like to get it working if possible.

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