VariantMaster protocols

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VariantMaster specifications


Unique identifier OMICS_02261
Name VariantMaster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM, VCF
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.02
Stability Stable
Maintained Yes



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  • person_outline Federico Andrea Santoni <>

Publication for VariantMaster

VariantMaster in pipeline

PMCID: 4006744
PMID: 24784881
DOI: 10.1371/journal.pgen.1004340

[…] reference for the calculation of coverage and reads on target. all experiments were performed using the manufacturer's recommended protocols without modifications., results were analyzed using the variantmaster software in order to identify de novo variants as well as variants respecting different mendelian inheritance models (dominant with reduced penetrance, recessive, x-linked). variant […]

VariantMaster in publications

PMCID: 5309803
PMID: 28176794
DOI: 10.1038/ncomms14279

[…] duplications of the genome. minor allele frequency was then checked on exome variant server ( and exac ( databases, as well as in variantmaster in geneva, to further filter for variants common among the affected individuals. final filtered variants were evaluated individually based on the predicted pathogenicity scores provided […]

PMCID: 4242613
PMID: 25420024
DOI: 10.1371/journal.pone.0112745

[…] “in-house” pipeline running on the vital-it ( center for high-performance computing of the swiss institute of bioinformatics (sib) ., de novo variants were identified using variantmaster . practically, heterozygous variants detected in the proband with samtools and pindel quality scores ≥100 and ≥600, respectively were retained for subsequent analysis. these variants […]

PMCID: 4006744
PMID: 24784881
DOI: 10.1371/journal.pgen.1004340

[…] variants (dgv) as benign (data not shown). we then performed targeted exon capture and next-generation sequencing on dna from the 46,xy dsd proband and her parents (). variants were evaluated using variantmaster , for de novo, x-linked and recessive models ()., snv: single nucleotide variant., *the target is the total protein coding sequence of the human genes according to refseq., maf: minimum […]

VariantMaster institution(s)
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
VariantMaster funding source(s)
Supported by grants from the SNF (144082), ERC (249968), ChildCare and Gebert Foundations, and a grant from the Bodossaki Foundation.

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