gravatar for Jordan

4 hours ago by

Pittsburgh

Hi,

I'm working on WGS data using cnvkit. I filtered the segments using segmetrics and 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!

link

written
4 hours ago
by

Jordan1.1k



Source link