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.
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.
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.
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.
Jongkyu Kim ([email protected])