RASQUAL specifications

Information


Unique identifier OMICS_18196
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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Maintainer


  • person_outline Natsuhiko Kumasaka <>

RASQUAL article

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

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