RASQUAL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RASQUAL

Tool usage distribution map

This map represents all the scientific publications referring to RASQUAL per scientific context
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RASQUAL specifications


Unique identifier OMICS_18196
Alternative name Robust Allele-Specific Quantitation and Quality Control
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A fragment (read) count table, with sample specific offsets (such as library size) and a VCF file with *phased* SNP genotypes and allele-specific counts.
Input format VCF
Output data Feature ID, rs ID, Chromosome, SNP position, Ref allele, Alt allele, Allele frequency, HWE Chi-square statistic, Imputation quality score (IA), Log_10 Benjamini-Hochberg Q-value, Chi square statistic (2 x log Likelihood ratio), Effect size (Pi), Sequencing/mapping error rate (Delta), Reference allele mapping bias (Phi), Overdispersion, SNP ID within the region, No. of feature SNPs, No. of tested SNPs, No. of iterations for N/A hypothesis, No. of iterations for alternative hypothesis, Random location of ties (tie lead SNP; only useful with -t option), Log likelihood of the N/A hypothesis, Convergence status (0=success), Squared correlation between prior and posterior genotypes (fSNPs), Squared correlation between prior and posterior genotypes (rSNP).
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Natsuhiko Kumasaka

Publication for Robust Allele-Specific Quantitation and Quality Control

RASQUAL citation


TCF21 and the environmental sensor aryl hydrocarbon receptor cooperate to activate a pro inflammatory gene expression program in coronary artery smooth muscle cells

PLoS Genet
PMCID: 5439967
PMID: 28481916
DOI: 10.1371/journal.pgen.1006750
call_split See protocol

[…] two-pass mapping. To avoid allele-specific mapping bias, we removed potentially mismapped reads using WASP. Read counts and FPKM values were generated using RNAseQC. Expression eQTL were mapped with RASQUAL. To remove potential confounders, we included gender, first 3 principal components inferred on the genotypes and first 8 PEER factors inferred on 10,000 highest expressed genes. Transcription […]

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RASQUAL institution(s)
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK

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