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HMZDelFinder specifications

Information


Unique identifier OMICS_16976
Name HMZDelFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED, RPKM, VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Requirements
GenomicRanges, DNAcopy, hmzdelfinder, rsubread
Maintained Yes

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Documentation


Maintainer


  • person_outline James Lupski

Publication for HMZDelFinder

HMZDelFinder citations

 (3)
call_split

Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

2017
Genome Med
PMCID: 5664429
PMID: 29089047
DOI: 10.1186/s13073-017-0482-5
call_split See protocol

[…] p://exac.broadinstitute.org/ dbNSFP, http://varianttools.sourceforge.net/Annotation/DbNSFP OMIM, http://www.omim.org/ University of California Santa Cruz (UCSC) Genome Browser, http://genome.ucsc.edu HMZDelfinder, https://github.com/BCM-Lupskilab/HMZDelFinder ClinVar, https://www.ncbi.nlm.nih.gov/clinvar/ Human Gene Mutation Database (HGMD), http://www.hgmd.cf.ac.uk/ac/index.php […]

library_books

Lessons learned from additional research analyses of unsolved clinical exome cases

2017
Genome Med
PMCID: 5361813
PMID: 28327206
DOI: 10.1186/s13073-017-0412-6

[…] ated CNVs; these tools detect a clinically relevant intragenic CNV when at least three contiguous exons are deleted [, ]. Therefore, in addition to these algorithms, we developed an in-house pipeline HMZDelFinder (https://github.com/BCM-Lupskilab/HMZDelFinder) [] to detect potential homozygous and hemizygous small intragenic deletions from WES data, including single exon “dropout alleles” that may […]

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Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate

2016
BMC Med Genomics
PMCID: 4950750
PMID: 27435318
DOI: 10.1186/s12920-016-0208-3

[…] We used CoNIFER [], CoNVex, and HMZDelFinder to predict potential heterozygous and homozygous CNVs based on exome data. Although many subjects have been pre-screened with karyotyping and array CGH, this bioinformatics approach enabl […]


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HMZDelFinder institution(s)
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway; Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children’s Hospital, Houston, TX, USA
HMZDelFinder funding source(s)
This work was supported in part by the National Human Genome Research Institute/National Heart Lung and Blood Institute [U54HG006542]; National Human Genome Research Institute grant to Baylor College of Medicine Human Genome Sequencing Center [U54HG003273]; National Institute of Neurological Disorders and Stroke [R01NS05829]; NHGRI, NHBLI, NINDS, all Institutes of the United States National Institutes of Health, the Polish National Science Centre [2014/13/B/NZ2/01248], and the Cancer Prevention & Research Institute of Texas training Program [RP140102].

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