PyroHMMvar specifications


Unique identifier OMICS_00069
Name PyroHMMvar
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input data An alignment file.
Input format BAM
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.
Biological technology Life Technologies, Roche
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Version 2.0.4
Stability Stable
Samtools library libbam.a
Maintained Yes




No version available


  • person_outline Rui Jiang
  • person_outline Ting Chen

Publication for PyroHMMvar

PyroHMMvar institution(s)
Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China; Computational Biology and Bioinformatics Program, University of Southern California, Los Angeles, CA, USA
PyroHMMvar 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).

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