Skip to main content


Variant Annotation and Filter Tool


The identification of disease-causing mutations in human genetics remains challenging despite the NGS revolution as up to 70% of cases are still unsolved. To tackle this challenge, we developed the VarAFT software to improve annotation and filtration steps.

VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples may be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique features including data from OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP that can be combined to optimally select candidate pathogenic mutations.

VarAFT is a standalone and multiplatform (Windows, Mac, Unix) system which is easy to install and easy to use. It does not require skills in informatics or a powerful computer.

VarAFT is developed by the Genetics and Bioinformatics team at INSERM UMR 1251 in the Medical School of la Timone Aix-Marseille University in Marseille, France. (More information on The VarAFT system is freely available to non-commercial users.

If you are using VarAFT in your projects, please cite: JP Desvignes & al Nucleic Acids Research, gky471,

Latest Changes

Version 2.17-2: July 10th, 2020
  • Fix issues on coverage analysis module. Human readable coverage file text output

  • Version 2.17-1: May 25th, 2020
  • Solve issue with coverage analysis

  • Version 2.17: May 20th, 2020
  • New API for Human Splicing Profesionnal from Genomnis SAS
  • Update data : ClinVar, Cosmic, OMIM, HPO, KEGG, REACTOME, PID, Gene Ontology, RefSeq, Ensembl
  • Update bed filefor coverage analysis
  • Solved proxy issue (Beta)
  • Add Varsome link
  • Solve minor issues

  • Version 2.16: May 7, 2019
  • New GnomAD version (2.11)
  • Add Iranome DB
  • Updated annotation(HPO,OMIM,Clinvar,Cosmic,RefGene)
  • Improve result table (display genotype information only for one sample or Trio, code color for prediction tools, font size customizable
  • Improve IGV connexion
  • Add proxy configuration (Beta)
  • Optimize auto filtering module
  • Solve minor issues

  • Version 2.15-2: March 19th, 2019
  • Solved issue with multi samples file analysis

  • Version 2.15-1: March 8th, 2019
  • Solved UMD-Predictor issue with latest Ensembl update
  • Improve gene checking during upload
  • Solved various minor issues

  • Version 2.15: January 4th, 2019
  • Update data : ClinVar, Cosmic, OMIM, HPO, KEGG, REACTOME, PID, Gene Ontology, RefSeq, Ensembl
  • Update bed filefor coverage analysis
  • Improve coverage analysis with file compression and new index
  • Coverage Analysis available for all exons and/or flanking region (+/-50bp)
  • Next update for annotation as Refseq, Ensembl, Clinvar, Cosmic ... will be available without waiting a new VarAFT release
  • Solved various minor issues
  • Version 2.14: September 17th, 2018
  • Solved issue with download
  • Solved issue with dblocal creation
  • Solved issue with auto filtering module

  • Version 2.13-1: May 2nd, 2018
  • Solved issue with dbsnp 150 download
  • Solved issue with configuration file

  • Version 2.13: April 27th, 2018
  • The documentation has been updated
  • Filtration based on Ensembl gene models for the impact of variants
  • Implementation of Annovar "Separate" option
  • Coverage analysis for RNA-seq BAM files
  • Speed improvement for file unzipping after download
  • Compliant with vcf.gz files
  • Minor issues solved ...

  • Version 2.12-1: March 7th, 2018
  • Solved issue for CNV Analysis
  • Solved issue for dblocal filtering
  • Solved issue for analysis of annotated files from version 2.06

  • Version 2.12: February 05, 2018
  • Automatic Annotation with Human Splicing Finder (Need Registration to the API)
  • Filtration with Human Splicing Finder
  • Updated data : ClinVar, Cosmic82, OMIM, HPO, KEGG, REACTOME, PID, Gene Ontology
  • New Frequency Filter Button
  • Solved any issues ...

  • Version 2.11-1: October 05, 2017
  • Solved issue with multisample VCF Annotation

  • Version 2.11: October 03, 2017
  • Add dbsnp 150 (from dbsnp download module)
  • Solved issue with CVN annotation
  • Solved issue with UMD-Predictor Webservice

  • Version 2.10.2: September 06, 2017
  • Solved issue with 1000G filter option

  • Version 2.10.1: August 25, 2017
  • Documentation Update
  • Solved issue with display options

  • Version 2.10: August 2017
  • Annovar Update
  • New data from dbNSFP3.3, gnomAD, GME DB
  • Update data (OMIM,Gene Ontology,KEGG..)
  • New module with HPO
  • New Pathway/HPO filter module
  • Filter based on a BED file
  • New Download Module
  • New Auto Filtering Module
  • Annotation and filtration of CNV data
  • Compatibility with previous annotated files

  • Version 2.06: February 2017
  • corrects a major issue with varaft server connection, specially for the first utilisation

  • Version 2.05: November 2016
  • Update Documentation (pdf)
  • Bugs Correction for export in varaft format
  • OMIM update
  • Use HSF webservice (beta version)
  • Solved issues with the conf file and settings

  • Version 2.04: August 2016
  • Better performance for Coverage Analysis in custom mode
  • Bug correction for the associated action of button "Get Compound Heterozygous" in the Filter Module

  • Version 2.00: June 2016
  • HG38 available (New ANNOVAR Version)
  • New Data Available (Kaviar, HRCR, OMIM ...)
  • Create your own local snp database
  • Coverage Analysis Module Optimized
  • Multithreaded process
  • VCF Multi Samples allowed
  • Tissues Expression from GTEx
  • Various gene score (RVIS, GDI, LoF, GHIS)
  • DMG, DEB and RPM availables for installation
  • and more ...
  • Download



    This video shows you how to set VarAFT.

    Download Database

    This video shows you how to download Annovar database.


    This video shows you how to annote your VCF.

    TRIO Recessive Analysis

    This video shows you how to analyze a TRIO.

    Coverage Analysis

    This video shows you how to perform a coverage analysis.

    Anemia Use Case

    This video shows you how to analyze the anemia use case.

    NA11919 Use Case

    This video shows you how to analyze the NA11919 use case.

    Use Cases


    Different reasons can explain that:
    • Depending on your system, the time required for IGV to load differs. So if you constat the BAM file never load, launch first IGV prior to the analysis.
    • If you try to upload a BAM file present on a distant server you need to upload it into IGV directly on IGV.
    • Check if the bai file corresponding to your bam file is present in the same directory.
    By default, VarAFT uses 4GB of RAM. If your system has less than 4GB of RAM and/or is a 32bits system you need to launch VarAFT with the VarAFT_min.exe file present in the VarAFT directory. However you should know that some options will be disabled such as Coverage analysis for whole exome and multi samples (>6) analysis in CUSTOM (without prefiltered files).
    To solve this issue, remove or rename the varaft.conf file situated in your user folder in VarAFT_conf folder. When you will restart VarAFT, this file will be regenerated by default.
    Due to the time limit of the generated token the analysis stops after a hour. In that case try to launch separetly the annotation of your files. Note that if your file was already annotated, you can use the "Human Splicing Finder Module" to only retrieve HSF annotation. This issue will be resolved in a next release.

    Our Tools

    More used Tools

    umdP hsf

    More Tools, see our web site


    Contact US

    They used VarAFT

    A novel EXT2 mutation in a consanguineous family with severe developmental delay, microcephaly, seizures, feeding difficulties, and osteopenia extends the …
    L El-Bazzal & al - EU of Genetics - 2019

    A severe clinical phenotype of Noonan syndrome with neonatal hypertrophic cardiomyopathy in the second case worldwide with RAF1 S259Y neomutation
    H Jaouadi & al - Genetics Research - 2019

    First Report of Diabetes Phenotype due to a Loss-of-Function ABCC8 Mutation Previously Known to Cause Congenital Hyperinsulinism
    T Koufakis & al - Case Reports in Genetics - 2019

    MRPS25 mutations impair mitochondrial translation and cause encephalomyopathy
    E Bugiardini & al - Human Molecular Genetics - 2019

    Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2
    Pekkinen M. & al - JCI Insight - 2019

    Identification of a ERCC5 c.2333T>C (L778P) Variant in Two Tunisian Siblings With Mild Xeroderma Pigmentosum Phenotype
    Chikhaoui A. & al - frontiers in Genetics - 2019

    Piezo1 is required for outflow tract and aortic valve development
    Fauchere A. & al - bioRxiv - 2019

    The added value of WES reanalysis in the field of genetic diagnosis: lessons learned from 200 exomes in the Lebanese population
    Jalkh N. & al - BMC Medical Genomics - 2019

    Genetic characterization of suspected MODY patients in Tunisia by targeted next-generation sequencing
    Dallali H. & al - Acta Diabetologica - 2019

    Retrospective study of 75 children with peripheral inherited neuropathy: Genotype–phenotype correlations
    Hoebeke C. & al - Archives de Pédiatrie - 2018

    Loss of calmodulin-and radial-spoke-associated complex protein CFAP251 leads to immotile spermatozoa lacking mitochondria and infertility in men
    Auguste Y. & al - The American Journal of Human Genetics - 2018

    RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases
    Lochmüller H. & al - European Journal of Human Genetics - 2018

    Phenotypic expression of a spectrum of Neurofibromatosis Type 1 (NF1) mutations identified through NGS and MLPA
    Tsipi M. & al - Journal of the Neurological Sciences - 2018

    Genetic variants in components of the NALCN–UNC80–UNC79 ion channel complex cause a broad clinical phenotype (NALCN channelopathies)
    Nuria C. Bramswig & al - Human Genetics - 2018

    Clinical profile of comorbidity of rare diseases in a Tunisian patient: a case report associating incontinentia pigmenti and Noonan syndrome
    Ghedira N. & al - BMC Pediatrics - 2018

    Novel ALPK3 mutation in a Tunisian patient with pediatric cardiomyopathy and facio-thoraco-skeletal features
    Jaouadi H. & al - Journal of Human Genetics - 2018

    Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses
    Medina-Carmona E. & al - Human Molecular Genetics - 2018

    Molecular diagnosis of inherited peripheral neuropathies by targeted next-generation sequencing: molecular spectrum delineation
    Bacquet J. & al - BMJ Open - 2018

    A novel EXT2 mutation in a consanguineous family with severe developmental delay, microcephaly, seizures, feeding difficulties, and osteopenia extends the phenotypic spectrum of autosomal recessive EXT2-related syndrome (AREXT2)
    El-Bazzal L. & al - European Journal of Medical Genetics - 2018

    Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility
    Esteve C. & al - The American Journal of Human Genetics - 2018

    Keratoendotheliitis Fugax Hereditaria: A Novel Cryopyrin-Associated Periodic Syndrome Caused by a Mutation in the Nucleotide-Binding Domain, Leucine-Rich Repeat Family, Pyrin Domain-Containing 3 (NLRP3) Gene
    Joni A. Turunen & al - American Journal of Ophthalmology - 2018

    Missense mutation of TTC7A mimicking tricho-hepato-enteric (SD/THE) syndrome in a patient with very-early onset inflammatory bowel disease
    João Farela Neves & al - European Journal of Medical Genetics - 2017

    Exome sequencing identifies recurrent BCOR gene alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell Lymphoma
    L Jallades & al - Haematologica - 2017

    Macrothrombocytopenia and dense granule deficiency associated with FLI1 variants: ultrastructural and pathogenic features
    Paul Saultier & al - Haematologica - 2017

    Exome sequencing reveals a de novo POLD1 mutation causing phenotypic variability in mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL)
    S Elouej & al - Metabolism - 2017

    Exome sequencing identifies two variants of the alkylglycerol monooxygenase gene (AGMO) as a cause of relapses in visceral leishmaniasis in children, in Sudan.
    S Marquet & al - The Journal of Infectious Diseases - 2017

    Genetic Characterization of a French Cohort of GNE-mutation negative inclusion body myopathy patients with exome sequencing
    M Cerino & al - Muscle & Nerve - 2017

    Le séquençage d'ADN à haut débit en pratique clinique
    C Lacoste & al - Archives de Pédiatrie - 2017

    A heterozygous ZMPSTE24 mutation associated with severe metabolic syndrome, ectopic fat accumulation, and dilated cardiomyopathy
    D Galant & al - Cells - 2016

    How to identify pathogenic mutations among all those variations: variant annotation and filtration in the genome sequencing era
    D Salgado & al - Human Mutation - 2016

    Clinical Interpretation of Variants from Next‐Generation Sequencing: The 2016 Scientific Meeting of the Human Genome Variation Society
    WS Oetting & al - Human Mutation - 2016

    Coverage analysis of lists of genes involved in heterogeneous genetic diseases following benchtop exome sequencing using the ion proton
    C Lacoste & al - Journal of Genetics - 2016

    Novel heterozygous mutation in ANO3 responsible for craniocervical dystonia
    M Miltgen & al - Movement Disorders - 2016

    Comparing targeted exome and whole exome approaches for genetic diagnosis of neuromuscular disorders
    S Gorokhova & al - Applied & Translational Genomics - 2015

    A mutation in the Gardos channel is associated with hereditary xerocytosis
    R Rapetti-Mauss & al - Blood - 2015

    Exome sequencing as a second-tier diagnostic approach for clinically suspected dysferlinopathy patients
    M Bartoli & al - Muscle & Nerve - 2014