Hi, I'm using WES data of tumor samples to find out CNV using CNVkit. My input data was re-calibrated BAM (recal.bam) files for CNVkit. I've used CNVkit's batch command (https://cnvkit.readthedocs.io/en/stable/pipeline.html) to generate CNV profile. The output looks like this.
Then I used few stringent threshold of log2 copy ratio and used several commands (segmetrics, genemetrics) to refine the noises and the the output was like this. This data is still noisy. In the CNVkit documentation it is recommended that to decrease noises we need to lower the bin number, but I didn't find any command for that. The plot looks like this.
After getting this data, I tried to find out the plots for individual chromosome level. I used this command for that: ~/cnvkit$ cnvkit.py scatter Tumor.cnr -s Tumor.cns -c chr8:80000000-120000000 -g PDP1,POP1 -o chr8.jpg --segment-color red Showing 2427 probes and 2 selected genes in region chr8:79999999-120000000 Wrote chr8.jpg The plot looks like this.
~/cnvkit$ cnvkit.py scatter Tumor.cnr -s Tumor.cns -c chr8 -g PDP1,POP1 -o chr8_2.jpg --segment-color red Showing 11090 probes and 2 selected genes in region chr8 Wrote chr8_2.jpg The plot looks like this. I don't know how to fix this. It's been 8 months I'm trying to fix this. Moving from one to another tool. I will be highly thankful if anyone can help me.