JAX-CNV: clinical-graded copy number variation detector

Overview

Here we present JAX-CNV, a newly developed NGS-based CNV algorithm and its performance on WGS data. We focused on deletions and duplications that are >50Kb.

Dependencies

To run the tool, the following dependencies are required

• Linux/Unix 64-bit
• gcc version 4.9 or higher
• zlib
• autoconf version 2.69 or higher

JAX-CNV depends on the following tools, which are already included in JAX-CNV/lib/

• fastaq Github
• jellyfish-2.2.6 Github
• htslib Github

Download and Installation

git clone --recursive https://github.com/wanpinglee/JAX-CNV.git
cd JAX-CNV
make

Usages

Kmer FASTA file preparation

We employ jellyfish to check 25-mer counts and GrabJellyfishKmer to dump a kmer FASTA file. Please check jellyfish for more jellyfish options, such as --threads/-t (Number of threads) and --Files/-F (Number files open simultaneously). -s is for Initial hash size and please adjust it for your machine.

bin/jellyfish count -m 25 -s <INT> -o <FASTA>.jf [-t <INT> -F <INT>] <FASTA>
bin/JAX-CNV GrabJellyfishKmer --ascii -i <FASTA>.jf -f <FASTA> -o <FASTA>.kmer

Detect CNVs

A sorted BAM, FASTA and Kmer are required. The results will be printed on stdout or use -o to specify an output file.

bin/JAX-CNV GetCnvSignal -f <FASTA> -k <FASTA>.kmer -b <BAM> --chrom $(seq -s \",\" -f \"chr%g\" 1 22),chrX,chrY [-o <OUTPUT>]
Rscript --vanilla JaxCNVMerge.R -i <OUTPUT>.bed

.bed.merge.bed is the final result. JaxCNVMerge.R could be also applied for other tools'' bed files.

The complete command line options are:

USAGE: GetCnvSignal -f <FASTA> -k <kmer_table> -b <BAM>

        -h --help                       Print this help list.

Input & Output:
        -b --bam <BAM/CRAM>             Input BAM or CRAM; required.
        -k --kmer <kmer_table>          Kmer table.
        -f --fasta <FASTA>              FASTA for kmer lookup.
        -o --output <FILE>              Output file.

Operations:
        -c --coverage <INT>             The expected coverage.
        -r --region chr:begin-end       A target region.
        -q --aln_qual                   A mapping quality filter for alignments. [40]
        --bin <INT>                     Report a result for each # bp. [50]
	--check_cov_only                Calculate coverages of chrmosomes; no CNV calling. [false]
	--chrom <STRING>		For example, --chrom chr1,chr2 or --chrom $(seq -s "," -f "chr%g" 1 22),chrX,chrY.
        --kmer_score <FLOAT>            Score for log2(kmer count) = 2 positions. [0.1]
        --log <FILE>                    Log output.
        --unique_kmer <FLOAT>           Require percentage of unique kmer to report a CNV. [0.6]

For Dcoker users

Dockerfile is provided. Please notice that sudo may be required for docker usages depending on your machine setting.

cd JAX-CNV
docker build .

JAX-CNV wnd jellyfish will be built on /tools in docker. Or, Pull docker image from wanpinglee/jax-cnv.

docker pull wanpinglee/jax-cnv:latest