/cytocad

Large copy-number variation detector using low-depth whole-genome sequencing data

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

CytoCAD is currently a work in progress. Please use the CNV calling subworkflow here instead.

CytoCAD - Copy-number variation caller using low-depth whole-genome sequencing data

Build Status PyPI pyversions PyPI versions Conda Github release PyPI license

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CytoCAD is a bioinformatics tool for the identification of large genomic copy-number variation through coverage anomaly detection (CAD) using mapped whole-genome sequencing (WGS) data. It has been tested in low-depth (~8X) Oxford Nanopore WGS long-read data. Its output displays chromosome illustrations demarcating regions of copy-number gains (Red) or losses (Blue). The above illustration shows a loss of one chromosome 7 copy, a gain of one chromosome 21 copy, a partial duplication of both chromosome 8 copies, and a loss of one chromosome 17 short arm. It also has two X chromosomes and no Y chromosome, suggesting a female sex.

Basic information:

  • Takes as input a mapped whole-genome sequencing BAM file and output a BED file and a chromosome ideogram-like figure
  • Uses Ruptures python package for change point detection of read coverage data per chromosome
  • Uses tagore for chromosome ideogram illustrations

Getting Started

Quick run

cytocad [Options] sample.bam working_dir
Argument Comment
sample.bam Input mapped WGS BAM file
working_dir Working directory

Output

Output file Comment
${sample}.ideo.svg Chromosome ideogram produced by tagore
${sample}.CNV.bed BED file of chromosome regions with CNV

For more information, see wiki.

Operating system:

  • Linux (x86_64 architecture, tested in Ubuntu 16.04)

Installation:

There are three ways to install CytoCAD:

Option 1: Conda (Recommended)

# Installing from bioconda automatically installs all dependencies 
conda install -c bioconda cytocad

Option 2: PyPI (See dependencies below)

# Installing from PyPI requires own installation of dependencies, see below
pip install cytocad

Option 3: GitHub (See dependencies below)

# Installing from GitHub requires own installation of dependencies, see below
git clone https://github.com/cytham/cytocad.git 
cd cytocad
pip install .

Installation of dependencies

  • bedtools >=2.26.0
  • samtools >=1.3.0
  • rsvg-convert >=2.40.13

Please make sure each executable binary is in PATH.

1. bedtools

Please visit here for instructions to install.

2. samtools

Please visit here for instructions to install.

3. rsvg-convert
sudo apt-get update
sudo apt-get install librsvg2-bin

Versioning

See CHANGELOG

Citation

Not available yet

Author

License

This project is licensed under GNU General Public License - see LICENSE.txt for details.

Limitations

  • Chromosome pairs illustrated by tagore may resemble sister chromatids, but they are in fact homologous pairs
  • Phasing of CNVs for each chromosome homologous pair is not yet possible.
  • The default minimum size of detectable CNV is about 500 kb. It can be adjusted by the 'interval' and 'rolling' parameters following the equation: minimum size ~= interval*rolling
  • Other chromosomal structural variations, such as inversions, have to be detected by other tools, such as NanoVar. NanoVar has incorporated CytoCAD in its pipeline from version 1.4.0 onwards.