View Single Post
Old 05-11-2015, 04:15 PM   #21
etal
Member
 
Location: California

Join Date: Oct 2013
Posts: 23
Default

Hi wisekh,

The LOH functionality in CNVkit is described here:
http://cnvkit.readthedocs.org/en/lat...s.html#scatter

However, the "calls" are simply displayed visually -- the variant allele frequencies are plotted alongside the copy ratios, and a shift in VAF from 0.5 indicates LOH. I'm currently working on expanding this functionality to make it more useful.

To run the complete pipeline with a tumor-normal pair and make a plot of the copy number and LOH shifts together, follow the quick start guide here:
http://cnvkit.readthedocs.org/en/latest/quickstart.html

Separately from running the CNVkit "batch" pipeline, you'll need to call SNPs in the tumor sample in VCF format. Then use that VCF file as input to the CNVkit "scatter" command along with the .cnr and .cns files from the CNVkit pipeline to make the plot.

Hope that helps,
Eric
etal is offline   Reply With Quote