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.
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/
git clone --recursive https://github.com/TheJacksonLaboratory/genome_similarity.git
cd genome_similarity
makeWe 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
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> [-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> Input BAM; 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]
--log <FILE> Log output.
--unique_kmer <FLOAT> Require percentage of unique kmer to report a CNV. [0.6]
--kmer_score <FLOAT> Score for log2(kmer count) = 2 positions. [0.1]
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