either 'chrFiles' or 'GCcontentProfile' must be set even a normal BAM is provided.

BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

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either 'chrFiles' or 'GCcontentProfile' must be set even a normal BAM is provided. #113

Open sunjh22 opened 2 years ago

sunjh22 commented 2 years ago

@calkan @valeu I run the following commond, config file is copied from the template but chrFile= was commented since I want to provide a control sample. ~/data/biosoft/FREEC/src/freec -conf analysis/temp/freec/config_WGS.txt -sample analysis/mapped/sample1.bam -control analysis/mapped/control1.bam

But it throws an error "Error: with the current options, either 'chrFiles' or 'GCcontentProfile' must be set".

Do you have any suggestions about this?

Thank you.

valeu commented 2 years ago

The method will still attempt to normalize for the GC-bias, so please provide chrFile= Alternatively, you need to set forceGCcontentNormalization parameter to 0.