MiStrVar

MiStrVar (Micro Structural Variant Caller) is a computational tool for detecting micro structural variations based on one-end anchors (OEA) from paired-end Whole Genome Sequencing (WGS) reads.

How do I get MiStrVar?

Just clone our repository and issue the make command:

git clone --recursive https://git@bitbucket.org/compbio/mistrvar.git
cd mistrvar/pipeline && make

You can also download the latest version of MiStrVar directly from the Downloads link.

Note: You will need at least g++ 4.7 and Python 2.7 to compile the source code.

How do I run MiStrVar?

You can use

mistrvar/pipeline/mistrvar.py -h

to get a description of each parameter. For more details, please check doc/MiStrVar_manual.pdf.

Simulation Datasets Used for Evaluation

Please check this link to download the simulation datasets that we used for evaluating MiStrVar. The folder contains 2 data files:

1. SV.fastq.gz: a 3.3GB gzipped fastq file
2. chr1.fa: reference genome for chromosome 1 from GRCh37.

We also provide a checksum file md5.sum for checking file integrity.

To run MiStrVar on this dataset, type

./mistrvar.py -p my_project -r chr1.fa --files fastq=SV.fastq.gz

Feel free to change my_project to any name you want. Remember to specify the paths correctly for chr1.fa and SV.fastq.gz if you download these 2 files to a folder other than the one you run MiStrVar. The VCF file with the prediction results will be generated in my_project.

Contact & Support

Feel free to drop any inquiry to agawrons at sfu dot ca.