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Bis-SNP

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. At an average 30× genomic coverage, Bis-SNP correctly identified 96% of SNPs using the default high-stringency settings.

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Bis-SNP forum

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Bis-SNP classification

Bis-SNP specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
Tab-delimited text, VCF
Programming languages:
Java, Perl
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Input format:
BAM
Operating system:
Unix/Linux
License:
MIT License
Stability:
Stable

Bis-SNP distribution

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No versioning.

Bis-SNP support

Maintainer

  • Benjamin P. Berman <>

Credits

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Publications

Institution(s)

USC Epigenome Center, University of Southern California, Los Angeles, CA, USA; Genetics, Molecular and Cellular Biology Program, University of Southern California, Los Angeles, CA, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

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