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vtsyvina / CliqueSNV

MIT License
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Haplotypes don't add to 100% #10

Closed cvk1988 closed 3 years ago

cvk1988 commented 3 years ago

Hello, Your tool is amazing and intuitive to use. I am, however, having an issue with the tool frequency outputs. On our data, cliques assembly reports 3 haplotypes and the respective frequencies do not add to 100%. The dataset is a mock community of known composition. What could be a reason for this?

Screen Shot 2020-10-15 at 3 50 22 PM

I appreciate your tool and your help!

vtsyvina commented 3 years ago

Hello,

We have a filtering step where all haplotypes with frequency less than -tf parameter is deleted from the output. You can read about it in the README. By default a conservative strategy is chosen with 5% cutoff. You can lower this down to, let's say 1% but it is always a tradeoff when reading errors and other noise can get into results