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|Interface||Command line interface|
|Restrictions to use||None|
|Input data||BAM files|
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- person_outline Alberto Magi
Publication for H3M2
Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
[…] 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
[…] 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
[…] 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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