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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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run with multiple control files #128

Open lmanchon opened 1 year ago

lmanchon commented 1 year ago

--Hi,

is it possible to submit several control files such as:

[control]

mateFile = /work/BAMFILES/*.bam inputFormat = BAM mateOrientation = FR

thank you --

vinishavenugopal commented 1 month ago

Hi @lmanchon

Did you figure out how to use multiple control samples?

@valeu @calkan @matthdsm I'd like to use FREEC with 50-100 control samples. How do I add multiple control samples in the configuration file?

Thanks, Vinisha

valeu commented 1 month ago

Hi Vinisha, you can only use FREEC with one control sample and one test. You can provide them in the config file, or directly in the command line. https://boevalab.inf.ethz.ch/FREEC/tutorial.html#Example If you insist on using FREEC on many control samples, I suggest you simply merge the corresponding BAM files into one. Alternatively, you can consider the OncoCNV tool that extracts the first 3 principal components from all provided control files and creats a nice normalized CNV profile for amplicon-sequencing data.