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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




No version available


  • person_outline Federico Andrea Santoni

Publication for VariantMaster

VariantMaster citations


X linked primary ciliary dyskinesia due to mutations in the cytoplasmic axonemal dynein assembly factor PIH1D3

Nat Commun
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 […]


Exome Sequencing in 53 Sporadic Cases of Schizophrenia Identifies 18 Putative Candidate Genes

PLoS One
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 […]


Loss of Function Mutation in the Palmitoyl Transferase HHAT Leads to Syndromic 46,XY Disorder of Sex Development by Impeding Hedgehog Protein Palmitoylation and Signaling

PLoS Genet
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 […]

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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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