run with multiple control files

[lmanchon]

--Hi,

is it possible to submit several control files such as:

[control]

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

thank you --

[vinishavenugopal]

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]

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.