How to get the range of LOH?
2
1
Entering edit mode
4.3 years ago
Tonny ▴ 20

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 • 1.7k views
ADD COMMENT
1
Entering edit mode
4.3 years ago
Eric T. ★ 2.7k

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 COMMENT
0
Entering edit mode
3.4 years ago
Shixiang ▴ 80

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

ADD COMMENT

Login before adding your answer.

Traffic: 1585 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6