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Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA
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README.md Update README.md May 25, 2019

README.md

SViCT: Structural Variant detection in Circulating Tumor DNA

SViCT is a computational tool for detecting structural variations from cell free DNA (cfDNA) containing low dilutions of circulating tumor DNA (ctDNA).

Table of contents

  1. Installation
  2. Running SViCT
  3. Publication
  4. Contact & Support

Installation

BIOCONDA

SViCT can be istalled using conda package manager via bioconda channel:

conda install -c bioconda svict

Installation from Source

Prerequisite. You will need g++ 4.9 and higher to compile the source code.

To install SViCT, you first need to fetch it from the github repository. After downloading, change the current directory to the source directory svict and run make in the terminal to create the binary file svict.

git clone https://github.com/vpc-ccg/svict.git
cd svict
make

If you are interested in a particular version, after downloading the git repo, checkout that version and do make.

git clone https://github.com/vpc-ccg/svict.git
cd svict
git checkout v1.0.0
make

You can also go to releases page, click on the desired version and then click either Source Code (zip) or Source code (tar.gz) link to download the file. After decompressing it, you just switch to the svict directory and run make.

Running SViCT

SViCT requires coordinate-sorted BAM/SAM generated from Illumina reads (short read technologies) and reference genome FASTA files to run detections:

./svict -i [input] -r [reference]

The output will be written to out.vcf in the current folder.

Running Example

To test SViCT, please first download the following two files ( ~ 3GB in total):

curl -L https://ndownloader.figshare.com/files/12380225 --output sim.75.sorted.bam
curl -L https://ndownloader.figshare.com/files/10144653 --output Homo_sapiens.GRCh38.87.dna.chromosomes.fa

Type the following command to run svict:

./svict -i sim.75.sorted.bam -r Homo_sapiens.GRCh38.87.dna.chromosomes.fa -o out

The VCF file with the prediction results will be generated as out.vcf in the current directory. The output should be the same as original result.

You can always use

./svict -h

to get a description of all the parameters.


Publication

If you use SViCT in your publication, please cite the following article:

Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA. Alexander R Gawroński, Yen-Yi Lin, Brian McConeghy, Stephane LeBihan, Hossein Asghari, Can Koçkan, Baraa Orabi, Nabil Adra, Roberto Pili, Colin C Collins, S Cenk Sahinalp, Faraz Hach. Nucleic Acids Res. 2019 Apr 23;47(7):e38. doi: 10.1093/nar/gkz067

See the publication page for details about the experiements.

Contact & Support

To report any bugs or issues please refer to the issues page.

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