Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
gravatar for dariober
10 weeks ago by
Glasgow - UK
dariober9.9k wrote:

I'd like to bring to your attention cnv_facets, a command line tool for detecting copy number variant (CNV), based on the facets package (Shen R and Seshan VE, Nucleic Acid Res, 2016).

Recently I've been using the facets package for detecting CNVs in tumour-normal sample pairs. I think facets works great but facets being a collection of R functions (plus an external program to prepare the input), it requires manual interaction from the user and so it doesn't play well with a streamlined analysis pipeline.

cnv_facets wraps all the required steps, from BAM files to VCF output and summary plots, in a simple command line call:

cnv_facets.R -t tumor.bam -n normal.bam -vcf snps.vcf.gz -o tex

Installation can be done under regular user permission (no admin rights required) as:

git clone
cd cnv_facets
bash /dir/on/your/path

For more information, check out the README file. Feel free to use and report any bugs, comments, questions.

ADD COMMENTlink written 10 weeks ago by dariober9.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1486 users visited in the last hour