This is the Linux app named BisSNP whose latest release can be downloaded as BisSNP-1.0.0.jar. It can be run online in the free hosting provider OnWorks for workstations.
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BisSNP
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DESCRIPTION
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP
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. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj
Features
- SNP caller
- methylation caller
- Bisulfite-seq/NOMe-seq/RRBS
- genotyping
Audience
Science/Research
User interface
Command-line
Programming Language
Perl, Java
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/bissnp/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
