Bis-SNP
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Application data |
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| Created by | Liu Y (dnaase) |
|---|---|
| Biological application domain(s) | SNP detection, Genotyping, DNA methylation, Sequencing, Epigenetics |
| Principal bioinformatics method(s) | SNP calling, Bisulfite mapping, Methylation calling |
| Technology | Illumina |
| Created at | USC Epigenome Center |
| Maintained? | Yes |
| Input format(s) | BAM |
| Output format(s) | VCF, BED, BEDGRAPH, WIG |
| Software features | Accurate SNP and methylation calling in Bisulfite-seq/NOMe-seq/RRBS |
| Programming language(s) | Java, Perl |
| Software libraries | GATK |
| Licence | MIT |
| Operating system(s) | Linux, Mac OS X |
| Contact: | bberman@usc.edu |
Summary: BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously.
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