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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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how to generate a LogR file for unmatched tumour sample #151

Closed esraa-jamal closed 1 year ago

esraa-jamal commented 1 year ago

Hi, Thank you for the new updates.. I need you kind help in explaining more to me how can I generate LogR file for tumour sample without matched Normal ... and how to do mirroring for BAF file as you kindly mentioned in previous comment??

Thank you in advance

tlesluyes commented 1 year ago

Hi @esraa-jamal,

Can you please indicate which comment you are referring to?

As for generating logR for sequencing data from unmatched tumours, I'm not sure what the best approach would be at this stage. Maybe using a kind of panel of normals, maybe extracting logR using another tool, or maybe simply computing log2(T-mean(T)) would work. I haven't tested anything so far so hard to recommend any particular method. Also, once logR is obtained, please note that one would need to hack the ascat.predictGermlineGenotypes function, more information here.

Instead, for unmatched tumour samples, you might be interested in running our ASCAT.sc tool.

Cheers,

Tom.

tlesluyes commented 1 year ago

Hi @esraa-jamal,

@jdemeul created a pull request related to your question (https://github.com/VanLoo-lab/ascat/pull/153). This will soon be integrated into ASCAT, although additional experiments will be required for WES & TS.

I'll close this thread for now.

Cheers,

Tom.