BisSNP 0.82.2

A tool for genotyping in bisulfite treated massively parallel sequencing on Illumina platform
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BisSNP is a utility based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, RRBS and NOMe-seq) on Illumina platform.

BisSNP uses a 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 in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously.

Moreover, BisSNP works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate (90.88% sensitivity in C/T SNPs with 0.16% false positive rate, 98.51% sensitivity in non C/T SNPs with 0.16% false positive rate).

Cytosine calling could detect non-reference cytosine context because it's only based on reference context.

last updated on:
July 13th, 2013, 23:23 GMT
file size:
8.7 MB
developed by:
USC Epigenome Center
license type:
operating system(s):
Mac OS X
binary format:
Home \ Math/Scientific
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What's New in This Release:
  • Add an option (-notEncrypt) to output raw read ID into cpgreads files, which may cause the file to be very large.
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