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Calls single nucleotide polymorphisms (SNPs) and short indels for both Ion Torrent and 454 resequencing data. PyroHMMvar is a method that has two distinct features: (i) an HMM to formulate homopolymer errors and which can distinguish real signals from sequencing errors and thus improve the alignment of reads against the reference and (ii) a graph data structure that merges multiple aligned reads at a given locus into a weighted alignment graph. PyroHMMvar is also available as part of the toolkit PyroTools.

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PyroHMMvar classification

PyroHMMvar specifications

Software type:
Application/Script, Package/Module
Restrictions to use:
Input format:
Biological technology:
Life Technologies, Roche
Programming languages:
Computer skills:
Command line interface
Input data:
An alignment file.
Output data:
The chromosome name, the genomic coordinate started from '1', the variant category, homozygous or heterozygous, the reference allele, the called allele, the genotype posterior probability, the variant quality score, the median mapping quality within a window and the median base quality within a window.
Operating system:
MIT License
Samtools library libbam.a

PyroHMMvar distribution


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PyroHMMvar support


  • Rui Jiang <>
  • Ting Chen <>


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Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China; Computational Biology and Bioinformatics Program, University of Southern California, Los Angeles, CA, USA

Funding source(s)

Supported by National Basic Research Program of China (2012CB316504) (in part), the National High Technology Research and Development Program of China (2012AA020401), the National Natural Science Foundation of China (61175002 and 60805010), Tsinghua University Initiative Scientific Research Program, Center of Excellence of Genome Sciences: Genomic Analysis of the Genotype-Phenotype Map (NIH/HG 2 P50 HG002790-06), Robust and Portable Workflow-based tools for mRNA and Genome re-sequencing (NIH/NHGRI 1U01 HG006531-01) and Computational Analysis of Metagenomic Sequencing Data (NSF/DMS ATD 7031026).

Link to literature

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