what kind of files should be put in controlsDIr?

[leovam]

Hi

I have an issue to the tool with mode StartWithBam

perl CoNVaDING.pl \
    -mode StartWithBam \
    -inputDir PATH/TO/sample \
    -controlsDir /PATH/TO/normalBams \
    -outputDir PATH/TO/Result \
    -bed /PATH/TO/BEDfile

the normalBams folder contains multiple normal bam files, however, when I run the code, I got error:

Uncaught exception from user code:
	Directory specified by "controlsDir" parameter does not contain normalized coverage files.

Does anyone know how to fix it? What kind of file should be included in controlsDir? Thanks!

[ljohansson]

Dear Leovam,

Bam files should go into the inputDir. This holts for both the samples as the control samples. Using the flag
-useSampleAsControl the samples will be copied to both controlsDir and outputDir. In this case the controlsDir should be empty. Alternatively first process the controlbam files (via inputDir) and copy the normalized coverage files to the controlsDir. Then, process your sample.

More information can be found here: http://molgenis.github.io/CoNVaDING/

Regards,
Lennart