Tool:cnv_facets: somatic Copy Number Variant calling using the facets package
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2.9 years ago

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.

CNV facets somatic cancer command line Tool • 3.2k views

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