bissnp

We have hosted the application bissnp in order to run this application in our online workstations with Wine or directly.

Quick description about bissnp:

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: