bissnp to run in linux online online with Winfy

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

Quick description about bissnp to run in linux online:

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.

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