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H3M2 specifications


Unique identifier OMICS_11104
Name H3M2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data BAM files
Input format BAM
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Alberto Magi

Publication for H3M2

H3M2 citations


Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

BMC Genomics
PMCID: 5789638
PMID: 29378520
DOI: 10.1186/s12864-018-4489-0

[…] medium length ROH [, ]. However, with the sparse nature of the WES target design, long ROH detection is not possible. Specific software, like “homozygosity heterogeneous hidden Markov model (HMM)” or H3M2, was designed to deal with this type of data [].Accurate ROH calling requires high density SNP genome-wide scan data. A number of factors influence the quality of ROH calling, including the marke […]


Uniparental disomy determined by whole‐exome sequencing in a spectrum of rare motoneuron diseases and ataxias

PMCID: 5441426
PMID: 28546998
DOI: 10.1002/mgg3.285

[…] Due to the contiguous stretches of homozygosity created by isodisomy, it is now detectable from single nucleotide polymorphism‐based (SNP) data (Papenhausen et al. ). A novel computational algorithm, H3M2, has been adapted for the sparse, irregular SNP distribution of WES (Magi et al. ). In this study, we evaluate the feasibility of applying the H3M2 algorithm to the detection of UPD based on inde […]


Homozygous NOTCH3 null mutation and impaired NOTCH3 signaling in recessive early onset arteriopathy and cavitating leukoencephalopathy

PMCID: 4459822
PMID: 25870235
DOI: 10.15252/emmm.201404399

[…] out brain abnormalities. Having a normalized phyloP score of phylogenetic conservation across 100 vertebrates ≥ 0.95 (Liu et al, ). Being within large exomic homozygous regions as identified by the H3M2 program (Magi et al, ). Large homozygous regions have enhanced probability to harbor the causative mutation in the proband. The highest priority was given to homozygous regions > 5 Mb, which are […]


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H3M2 institution(s)
Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy; Diagnostic Genetic Unit, Careggi Hospital, Florence, Italy; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
H3M2 funding source(s)
This work was supported by the Italian Ministry of Health, Young Investigators Programme, Project GR-2009-1574072.

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