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tgen / lumosVar2

Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.
MIT License
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How to run primary/met tumor-only samples ? #6

Closed qindan2008 closed 3 years ago

qindan2008 commented 3 years ago

I have 10 pairs of primary/met samples from 10 patients, but none of them have normal samples. How to run lumosVar2 for somatic, gremline and CNV?

Thanks

rhalperin commented 3 years ago

For tumor-only mode, you just need NormalSample: 0 in your yaml. Then you just need the paths to both bams for a patient in your bamlist file, and an estimated tumor content for priorF for each sample in the yaml. If these are solid tumors and you don't have tumor content estimates, you can use priorF: [0.7;0.7]. Does that answer your question?

qindan2008 commented 3 years ago

yes, thank you very much