RASQUAL statistics

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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



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  • person_outline Natsuhiko Kumasaka <>

Publication for Robust Allele-Specific Quantitation and Quality Control

RASQUAL in publication

PMCID: 5439967
PMID: 28481916
DOI: 10.1371/journal.pgen.1006750

[…] 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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