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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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Challenges with adapting for long read data? #38

Closed tsa4002 closed 6 months ago

tsa4002 commented 8 months ago

Hi,

I'm curious what are the aspects of long read sequencing that make it difficult for use in somatic unpaired variant calling? Wouldn't the same general approach of identifying variants that are different at that location relative to the other cell types and the reference still apply?

Thanks

Francesc-Muyas commented 6 months ago

Dear user,

Despite the huge interest in detecting somatic variants in single-cell long-read data, the current version of SComatic does not support this type of variant calling. I hope we can develop this upgrade in the future.

Thanks, Fran

tsa4002 commented 6 months ago

Hi @Francesc-Muyas

Thank you for the reply. I understand SComatic's limitation, which other tools also have, i was hoping more that you could elaborate on why that limitation exists. I've rephrased my question and removed the aspects of how i've tried modifying SComatic to fit that use case.

Thanks