I'm working on WGS data using cnvkit. I filtered the segments using
call. Here are my steps:
cnvkit.py segmetrics tumor.cnr -s tumor.cns --ci --sem -o tumor.segmetrics.cns cnvkitpy call tumor.segmetrics.cns --filter ci -o tumor.segmetrics.call.cns
I have about 300 segments at the end of this step. Is there a way to tell, which are statistically the best segments?
For e.g., two rows in tumor.segmetrics.call.cns file looks like this.
chromosome start end gene log2 cn depth probes weight chr1 125086529 125146265 - 0.0648392 2 143.179 52 44.4282 chr1 125146265 125175570 - -1.35037 0 71.7419 24 14.5482
Is there a way to tell which segment you trust more? I understand that, more the weight better the reliability.
But I was wondering how you would normally pick the best segments?
Thanks in advance!