coverageMaster: CNV detection and visualization from NGS short reads

Quick Links

CoverageMaster (CoM) is a copy number variation (CNV) calling algorithm i ased on depth-of-coverage maps designed to detect CNVs of any size i n exome [whole exome sequencing (WES)] and genome [whole genome sequencing (WGS)] data. The core of the algorithm is the compression of sequencing coverage data in a multiscale Wavelet space and the analysis through an iterative Hidden Markov Model.

References:

Melivoia Rapti, Yassine Zouaghi, Jenny Meylan, Emmanuelle Ranza, Stylianos E Antonarakis, Federico A Santoni
CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications
Briefings in Bioinformatics, Volume 23, Issue 2, March 2022, bbac049, https://doi.org/10.1093/bib/bbac049 Published: 26 February 2022

Documentation

coverageMaster github page

Important Notes

Module Name: coverageMaster (see the modules page for more information)
Unusual environment variables set
- COM_HOME installation directory
- COM_BIN executable directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive -c 16 --mem 45g --gres=lscratch:20
[user@cn3144 ~]$ module load coverageMaster
[+] Loading singularity  3.8.5-1  on cn3144
[+]  Loading coverageMaster 20220706  ...
[user@cn3144 ~]$  coverageMaster.py -h 
Usage: coverageMaster.py [options] <cov_file> <stats_file> <gene list(file or comma separated gene names)|region(chr:start-end)> -r <reference.cov> -o <output_px>

Options:
  -h, --help            show this help message and exit
  -c CONTROL, --control=CONTROL
                        <optional> txt file with a control file per line (.cov
                        with .report.txt in same folder)
  -s SINGLE_CONTROL, --single-control=SINGLE_CONTROL
                        <optional> single control file (.cov with .report.txt
                        in same folder)
  -r REF, --ref=REF     reference file
  -o OUTPUT_PX, --out=OUTPUT_PX
                        output prefix
  -g CGD, --cgd=CGD     <optional> clinical genomic database
  -f, --force           <optional> force output
  -e EXONS, --exons=EXONS
                         <optional> n. of extra exons
  -x OFFSET, --offset=OFFSET
                         <optional> offset to ref
  -d WID, --width=WID    <optional> d*std
  -l LEV, --level=LEV    <optional> max wavelet level
  -m MINLEV, --minlevel=MINLEV
                         <optional> min wavelet level
  -w, --wig              <optional> write wig
  -b, --bed              <optional> BED input
  -k DGV, --dgv=DGV      <optional> DGV file
[user@cn3144 ~]$ git clone https://github.com/fredsanto/coverageMaster
[user@cn3144 ~]$ cd coverageMaster/DEMO
[user@cn3144 ~]$ gene=PGM1 && co=control.PGM1.cov && python ../coverageMaster.py test.PGM1.cov test.PGM1.report.txt $gene -s $co -r ref.PGM1 -o test.PGM1
Fri Sep  9 04:04:48 2022 - --------------------------------------------------------------------------------
CoverageMaster is warming up
Fri Sep  9 04:04:48 2022 - Query index created
Fri Sep  9 04:04:48 2022 - Reference index created
Fri Sep  9 04:04:48 2022 - Processing Gene: XIST - Region chrX:73040485-73072588
chrX not in my list - skipped
/opt/conda/envs/coveragemaster/lib/python3.6/site-packages/numpy/core/fromnumeric.py:3118: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/opt/conda/envs/coveragemaster/lib/python3.6/site-packages/numpy/core/_methods.py:85: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Fri Sep  9 04:04:48 2022 - Control index created
Fri Sep  9 04:04:48 2022 - Processing Gene: XIST - Region chrX:73040485-73072588
chrX not in my list - skipped
Fri Sep  9 04:04:48 2022 - Loop with control control.PGM1.cov
Fri Sep  9 04:04:48 2022 - Processing Gene: PGM1 - Region chr1:64058946-64125916
Fri Sep  9 04:04:48 2022 - Processing Gene: PGM1 - Region chr1:64058946-64125916
Fri Sep  9 04:04:48 2022 - PGM1:Zooming 4
Fri Sep  9 04:04:48 2022 - PGM1:Zooming 3
Fri Sep  9 04:04:48 2022 - PGM1:Zooming 2
Fri Sep  9 04:04:48 2022 - PGM1:Zooming 1
user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$