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VaRank specifications

Information


Unique identifier OMICS_10061
Name VaRank
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format VCF
Output format TSV
Operating system Unix/Linux
Computer skills Advanced
Version 1.2.5
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Publication for VaRank

VaRank in publications

 (9)
PMCID: 5123056
PMID: 27882921
DOI: 10.1038/ncomms13586

[…] sequencing data processing and variant calling (snp and indels) with the genome analysis toolkit revealed 60,612 to 63,887 genetic variants per proband (). variant filtering was performed with the varank programme using stringent criteria excluding (i) non-pathogenic variants defined in dbsnp 138, (ii) variants represented with an allele frequency of more than 1% in dbsnp, the exome variant […]

PMCID: 4804614
PMID: 27004399
DOI: 10.1186/s13023-016-0408-0

[…] exome aggregation consortium (exac) []. recurrent variations found in more than 10 % of the patients in our cohort were also filtered. subsequent variant annotation and ranking was performed using varank v1.4.0 [] configured with alamut batch (interactive biosoftware)., gaps in ngs coverage of the targeted regions (i. e. coverage <30x, the threshold recommended in the literature [, ]), […]

PMCID: 4773637
PMID: 26973538
DOI: 10.3389/fphys.2016.00070

[…] company (casava 1.8, illumina and finally detects from 80965 to 82263 variants (snps and indels) per proband (table ). annotation, ranking, and filtering of genetic variants were performed with the varank program (geoffroy et al., ). very stringent criteria were used for excluding non-pathogenic variants, in particular: (1) variants represented with an allele frequency of more than 1% in dbsnp […]

PMCID: 5021520
PMID: 27623147
DOI: 10.7554/eLife.17163.012

[…] samtools v0.1.18 mpileup and samtools 0.1.7 pileup. variant quality scores were recalibrated using gatk. variants were annotated using snpeff v2.0.5, gatk v2.5.2 and snpsift v3.3c (, ). finally, varank () was used to rank discovered variants, which were filtered on homozygous state in the two affected patients. variants identified by exome sequencing were confirmed by sanger sequencing […]

PMCID: 4752661
PMID: 26502894
DOI: 10.1136/jmedgenet-2015-103302

[…] with the gatk toolkit v3.1 using hard-filtering parameters. variants were annotated using snpeffv.3.4. variant frequencies were compared with an internal exome database and prioritised using varank. variants were prioritised by allele frequency (<1% in the single nucleotide polymorphism database (dbsnp137), 1000 genomes database, exome variant server (evs) database and our internal […]


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VaRank institution(s)
Laboratoire de Génétique médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg, Strasbourg, France; IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France; Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Interactive Biosoftware, Rouen, France; Laboratoire ICUBE, UMR CNRS 7357, LBGI, Université de Strasbourg, Strasbourg, France
VaRank funding source(s)
This study was supported by grants and fellowships from Agence de Biomédecine, Fondation Jerome Lejeune, APLM, CREGEMES, INSERM and ANR-11-BSV1-026-01.

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