BisSNP Publisher's description
from USC EPIGENOME CENTER
BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated
It contains the following key features:
Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.);
Works for single end and paired-end;
Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing;
Based on Java map-reduce framework, allow multi-thread computing. Cross-platform;
Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysisl; simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser.
BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate 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. 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 is not only based on reference context, so it could detect non-reference cytosine context for usage in epigenome wide association study.
What's New in This Release:· Enable the output of low quality CpGs and reference CpGs(not called as CpG) in cpg.raw.vcf file.
· Fix the bug for wrong alleles display when there are try or more alleles.
· Fix the bug that call CpH methylation status improper on non-directional protocol BS-seq.
Program Release Status: New Release
Program Install Support: Install and Uninstall