JAX-CNV implemens an algorithm for copy number variant (CNV) calling from the whole-genome sequencing (WGS) data. On testing data, it demonstrated ~7-fold increase in the number of detected CNVs as compared to the chromosomal microarray assay (CMA) for clinical diagnosis.

References:

• Wan-Ping Lee, Qihui Zhu, Xiaofei Yang, Silvia Liu, Eliza Cerveira, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Kai Ye, Charles Lee, Chengsheng Zhang,
  JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level
  Genomics Proteomics Bioinformatics 20 (2022) 1197–1206

• JAX-CNV Github page

• Module Name: JAX-CNV (see the modules page for more information)
• Unusual environment variables set
  • JAX_CNV_HOME  installation directory
  • JAX_CNV_BIN       executable directory
  • JAX_CNV_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=12g -c8 --grep=lscratch:20
[user@cig 3335 ~]$ module load JAX-CNV
[+] Loading singularity  4.0.1   on cn3335
[+] Loading JAX-CNV  20240208
[user@cn3335 ~]$ JAX-CNV 

USAGE: /opt/conda/envs/jax_cnv/genome_similarity/bin/JAX-CNV  [options]

Commands:
        GrabJellyfishKmer       Report the count of kmer giving Jellyfish database and a FASTA.
        GetCnvSignal    Report CNV signals such as read depth and kmer count.

[user@cn3335 ~]$ JaxCNVMerge.R
...
The usage of JaxCNVMerge is like:
 "Rscript --vanilla JaxCNVMerge.R -md 3000000 -i filename". The output file is filename.merge.bed
 Arguments:
  --max_distance or -md  (option), numeric, distance threshold in merging, default s 3000000
  --bed or -i            (required), string, the bed file of the CNV fragments
  --help or -h,          print the help messge
[user@cn3335 ~]$ exit
user@biowulf]$