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A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and DNA methylation calling in bisulfite treated massively parallel sequencing. Uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine contextto determine genotypes and methylation levels simultaneously.


Biology, Genetics, Genotype and phenotype, Sequencing


  • Operation: SNP detection, Methylation analysis, Bisulfite mapping, SNP detection
  • Software interface: Command-line interface
  • Language: Java, Perl
  • Operating system: Linux, Mac OS X
  • License: The MIT License
  • Cost: Free
  • Version name: 1.0.0
  • Maturity: Mature
  • Credit: Benjamin P Berman
  • Contact: bberman at
  • Collection: -


Liu Y, Siegmund KD, Laird PW, Berman BP "Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data." Genome Biol. 2012; 13(7):R61
PMID: 22784381
PMCID: PMC3491382

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