BisSNP 0.82.2

A tool for genotyping in bisulfite treated massively parallel sequencing on Illumina platform

  Add it to your Download Basket!

 Add it to your Watch List!

0/5

Rate it!

What's new in BisSNP 0.82.2:

  • Add an option (-notEncrypt) to output raw read ID into cpgreads files, which may cause the file to be very large.
Read full changelog
report
malware
send us
an update
LICENSE TYPE:
Freeware 
FILE SIZE:
8.7 MB
USER RATING:
UNRATED
  0.0/5
DEVELOPED BY:
USC Epigenome Center
CATEGORY:
Home \ Math/Scientific
1 BisSNP Screenshot:
BisSNP
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 et.al. 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

Runs on: Mac OS X (-)

requirements

#parallel sequencing #genotyping tool #Illumina platform #parallel #sequencing #genotype #Illumina

Add your review!

SUBMIT