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HMZDelFinder specifications


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
GenomicRanges, DNAcopy, hmzdelfinder, rsubread
Maintained Yes



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  • person_outline James Lupski <>

Publication for HMZDelFinder

HMZDelFinder in publications

PMCID: 5664429
PMID: 29089047
DOI: 10.1186/s13073-017-0482-5

[…] , dbnsfp, , omim, , university of california santa cruz (ucsc) genome browser, , hmzdelfinder, , clinvar, , human gene mutation database (hgmd), , candidate […]

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

[…] 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 ( [] to detect potential homozygous and hemizygous small intragenic deletions from wes data, including single exon “dropout alleles” […]

PMCID: 4950750
PMID: 27435318
DOI: 10.1186/s12920-016-0208-3

[…] number, the maximum/minimum length, the median length, the mean length, and the total length of potential aoh regions (> = 0.5 mb)., we used conifer [], convex (sanger centre, unpublished), and hmzdelfinder ( to predict cnvs from wes data. hmzdelfinder is an in-house-developed algorithm implemented in the r programming language (r core team […]

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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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