MendelScan specifications

Information


Unique identifier OMICS_00065
Name MendelScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Maintainer


  • person_outline Daniel C. Koboldt <>

Publication for MendelScan

MendelScan in publications

 (3)
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] the gene function and hundreds of candidate variants need to be filtered. so, an improved workflow to identify potential candidate variants involved in the disease is needed. software package as mendelscan try to solve this providing a composite score improved with tissue expression data []. however, systemic disease or disease involving tissues with multiple cells types and low-quality gene […]

PMCID: 5455168
PMID: 28549094
DOI: 10.1167/iovs.16-21341

[…] v.2.0 (roche, madison, wi, usa) according to the manufacturers' protocols. illumina paired-end sequencing (2 × 100 bp), alignment, and variant calling were performed as described previously., mendelscan was used to rank single nucleotide variants (snvs) and indels based on a combination of segregation, population frequency, retinal expression, and predicted functional impact. the exome […]

PMCID: 4905677
PMID: 27294265
DOI: 10.1371/journal.pgen.1006090

[…] the exomes were analyzed using step-by-step filtering strategies (). the estimated fraction of shared variants by descent was calculated using the identity-by-descent method implemented by mendelscan version 1.2.1 (http://gmt.genome.wustl.edu/mendelscan) [] according to the autosomal dominant inheritance in family 1. genetic variants were first filtered to retain only non-synonymous […]


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MendelScan institution(s)
The Genome Institute at Washington University, St. Louis, MO, USA; Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA; Ocular Genomics Institute, Harvard Medical School, Boston, MA, USA; Hussman Institute of Human Genomics, University of Miami, Miami, FL, USA
MendelScan funding source(s)
Supported by the Foundation Fighting Blindness, the National Eye Institute (grant EY007142), and the National Human Genome Research Institute (grant HG003079).

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