From the LoFreq Wiki:
LoFreq is a fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. It is designed to robustly call low-frequency variants by exploiting base-call quality values. LoFreq has been used to call rare variants in viral and bacterial sequencing datasets and can be used to study mitochondrial heteroplasmy and rare somatic mutations in heterogeneous tumors.
LoFreq makes full use of base-call qualities, which are usually ignored by other methods or only used for filtering. It is very sensitive; most notably, it is able to predict variants below the average base-call quality. Each SNV call is assigned a p-value which allows for rigorous control of false positive rates. Even though it uses no approximations or heuristics it is very efficient due to several run-time optimizations. LoFreq is generic and fast enough to be applied to high-coverage data but also longer genomes. It takes a minute to analyse a Dengue genome sequencing data of nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and 1.5 hours to run on a 100X coverage human exome data.
The relevant publication is: Wilm et al. (2012). LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. (Advance access)
Source-code is available from the sourceforge project website
Version 0.3.1 includes a wrapper for calling somatic SNVs
Update: Dec 2014
- We've moved the website to github pages.
- MIT licensed source-code is now available on github
- LoFreq is now able to call indels, we've added a probabilistic realigner that fixes mapping errors etc. etc.