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QuASAR specifications


Unique identifier OMICS_06772
Alternative name Quantitative Allele Specific Analysis of Reads
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes






No version available



  • person_outline Francesca Luca
  • person_outline Roger Pique-Regi

Publications for Quantitative Allele Specific Analysis of Reads

QuASAR citations


Allele specific expression and methylation in the bumblebee, Bombus terrestris

PMCID: 5600721
PMID: 28929021
DOI: 10.7717/peerj.3798

[…] all the SNPs, before the SNPs were filtered based on mapping quality score (; ). Only SNPs with a mapping quality score of p < 0.05 and a read depth of ≥6 were included in the analyses.The R package, QuASAR implements a statistical method for: (1) genotyping from next-generation sequencing reads (according to the Hardy–Weinberg equilibrium), and (2) conducting inference on allele specific expressi […]


IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing

Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076

[…] hers (,,). However, either available phased genotypes (e.g. MMSEQ, asSeq and EMASE) or family trio data (e.g. AlleleSeq and Allim) are required for haplotyping using most of these applications. While QuASAR uses solely RNA-seq data, it can only perform ASE analysis at the single SNV level. MBASED is the only currently available tool for ASE analysis at the gene level using only RNA-seq data. Howev […]


Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota

PMCID: 5047527
PMID: 27709125
DOI: 10.1128/mSystems.00067-16

[…] ollowing analysis.Using samtools mpileup and the hg19 human reference genome, we obtained the read counts at each SNP in each sample from the RNA-seq data. These pileups were then processed using the QuASAR package () by combining the RNA-seq reads from each sample (as they are all derived from the same colonocyte cell line) for joint genotyping. From the genotype information we identified heteroz […]


Which Genetics Variants in DNase Seq Footprints Are More Likely to Alter Binding?

PLoS Genet
PMCID: 4764260
PMID: 26901046
DOI: 10.1371/journal.pgen.1005875

[…] n of which genetic variants in DNaseI sensitive regions are more likely to affect binding. To experimentally assess the accuracy of our answer, we used Quantitative Allele-Specific Analysis of Reads (QuASAR) [] to perform joint genotyping and ASH analysis within DNase I hypersensitivity (DHS) regions (). While the initial quality filtering is the same as for the CENTIPEDE analysis, the parameters […]


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QuASAR institution(s)
Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University Scott Hall, Detroit, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
QuASAR funding source(s)
Supported by the National Institute of Health [1R01GM109215-01] and the American Heart Association [14SDG20450118].

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