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4 hours ago by



I'm working on WGS data using cnvkit. I filtered the segments using segmetrics and call. Here are my steps: segmetrics tumor.cnr -s tumor.cns --ci --sem -o tumor.segmetrics.cns
cnvkitpy call tumor.segmetrics.cns --filter ci -o

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 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!


4 hours ago


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