Question: How to get the range of LOH?
1
gravatar for Tonny
2.9 years ago by
Tonny20
Shanghai, China
Tonny20 wrote:

Hi,

I need some help for the LOH in the output of CNVkit. How could I get the region of LOH for SciClone analysis? In the documentation I only find how to plot the LOH, and I'd like to get the detail information of these region.

cnvkit • 1.2k views
ADD COMMENTlink modified 24 months ago by Shixiang60 • written 2.9 years ago by Tonny20
1
gravatar for Eric T.
2.9 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

If you run the call sub-command with a VCF (see here), the output .cns file is a table with the columns cn1 and cn2. You can filter the rows for columns where cn1 != cn2 with awk, Excel, cnvlib, or any tool you like to get the segments with allelic imbalance. Those are the rows that are informative for SciClone analysis, I think.

ADD COMMENTlink written 2.9 years ago by Eric T.2.6k
0
gravatar for Shixiang
24 months ago by
Shixiang60
Shanghai
Shixiang60 wrote:

You can use SciClone without LOH info. Only SNV data is nessary, and it is better to include CNV data.

ADD COMMENTlink written 24 months ago by Shixiang60
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