BisSNP Bisulfite-seq/NOMe-seq SNPs and cytosine methylation caller
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BisSNP Description

BisSNP was specially developed as an useful tool that's based on the Genome Analysis Toolkit. BisSNP makes use of the Bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context for determining genotypes and methylation levels simultaneously. The software can work for single-end and paired-end reads. BisSNP is developed in the Java programming language. Main features: Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); Accurate variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis; simplified bedGraph, wig and bed format for visualization in UCSC genome browser and IGV browser.

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