RePlow

RePlow is a Java based variant caller designed for detecting somatic single nucleotide variants (SNVs) from the replicated set of high-depth sequencing data. RePlow is highly specialized for the identification of somatic mutations with low variant allele frequency (VAF ~1%). RePlow accurately detects such low-level mutations based on the probabilistic model that jointly analyzes library-level replicates, regardless of the sequencing platform. The important features of RePlow are:

• On-the-fly estimation of the VAF distribution of background errors
• Improved low-level SNV calling based on the estimated error profiles and the observation concordance between replicates