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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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Normal prefix in prepareHTS #100

Closed SusiJo closed 2 years ago

SusiJo commented 2 years ago

Hi,

I have a question regarding the naming of the germline logR and BAF files in the function prepareHTS: Why is the prepended prefix of these files the tumourname and not the normalname
see here?

tlesluyes commented 2 years ago

Hi @SusiJo,

This is because people may have multiple tumours and one single normal to compare to. If you were to run ASCAT in parallel, normal files (both logR and BAF) would be overwritten multiple times and may cause issues (e.g. one task reading a truncated file because it's being written). We prevent this by saying: paste0(tumourname,"_normalLogR.txt") is the normal logR of tumour tumourname. Please note that you can control filenames with both normalLogR_file and normalBAF_file if default names don't work well for you.

Cheers,

Tom.

SusiJo commented 2 years ago

Hi @tlesluyes,

Thanks for the quick reply!

Cheers