Adaption of the original PennCNV algorithm for whole-genome sequencing data
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README.md
convert_map2signal.pl
download_and_format_database.sh
hhall_loh.hmm
penncnv-seq_example.sh
penncnv2bed.py
svgen_simulations_penncnvseq.sh
wgs.hmm

README.md

PennCNV-Seq

Adaptation of the original PennCNV algorithm for whole-genome sequencing data.

PennCNV-Seq installation

Install PennCNV (at least version v1.0.4)

Releases can be found here. Installation instructions at http://penncnv.openbioinformatics.org/en/latest/user-guide/install/

Install BEDtools

Instructions at http://bedtools.readthedocs.io/en/latest/content/installation.html

Download PennCNV-Seq scripts

git clone git@github.com:WGLab/PennCNV-Seq.git
cd PennCNV-Seq

# Define your download options (run the command below to see the parameters)
./download_and_format_database.sh

Run PennCNV-Seq example

cd PennCNV-Seq
./penncnv-seq_example.sh [penncnv_dir] [penncnv_ref_dir] [genome_version] [population] [reference.fasta] [bam_file]

Visualize PennCNV results in genome browsers (IGV or UCSC website)

python penncnv2bed.py results.rawcnv > results.bed