I am using CNVkit to generate CNV calls. My question is, is it better to use base quality score re-calibrated bam file than original bam file?
My guess is it makes no difference. Does the documentation states one needs to perform base score recalibration in order to use CNVkit?
The document didn't mention this. I am sure CNVkit works without recalibration. I am just wondering if people usually do recalibration before running CNVkit.