joshuak94 / vaquita-lr

Identification of structural variations

Vaquita accurately identifies structural variations using split-reads, discordant read-pairs, soft-clipped reads, and read-depth information. Vaquita does not depend on external tools and very fast. You can analyze 50x WGS sample within an hour.

Download & Compile

git clone https://github.com/seqan/vaquita.git
mkdir vaquita-build && cd vaquita-build
cmake ../vaquita && make vaquita -j 4

Vaquita supports GCC≥4.9 and Clang≥3.8.

Usage

vaquita call -r [reference.fa] [input.bam] > [output.vcf]

The .bam file must be sorted by coordinate (eg. samtools sort). You can find more options using vaquita call --help.

Citation

Jongkyu Kim and Knut Reinert, Vaquita: Fast and Accurate Identification of Structural Variations using Combined Evidence. Workshop on Algorithmic Bioinformatics (WABI) 2017

DOI: 10.4230/LIPIcs.WABI.2017.13

• You can find all the scripts and information about raw datasets that I used for benchmarking at this repository.

Contact

Jongkyu Kim ([email protected])