cytocad 1.0.3

Description:

cytocad 1.0.3

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









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

Tham Cheng Yong - cytham

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.