SOAPsv is a program for detection of structural variation.
This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data.
- a. Sensitivity and Completeness
We can provide both conventional re-sequencing method based calls and unique variant calls that only can be detected by our assembly pipeline while achieving a relatively high sensitivity and low FP rate.
- b. Overcoming Length Limitations
Our method can overcome the insert-size limitation and reads’ gap-open-size limitation in variant calling process.
- c. Resolution
We report all the variant calls’ breakpoints at single base resolution.
- d. Genotype aware
Our result contains the information of exactly genotype for each variant calls.
Li Y, Zheng H, Luo R, Wu H, Zhu H, Li R, Cao H, Wu B, Huang S, Shao H, Ma H, Zhang F, Feng S, Zhang W, Du H, Tian G, Li J, Zhang X, Li S, Bolund L,Kristiansen K, de Smith AJ, Blakemore AI, Coin LJ, Yang H, Wang J, Wang J. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol. 2011 Jul 24;29(8):723-30. doi: 10.1038/nbt.1904.
You may get the updated SOAPsv from here
a) Intel CPU with SSE instructions
b) The program needs ~30G main memory to run with data from H. sapiens.
a) Unix/Linux System
b) The version of gcc compiler is at least 4.2.4
c) The version of perl is at least 5.8.5