CNVkit bam file
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?
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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.