SynthesisBioinformatics (Oxford, England)2020
RICOPILI: Rapid Imputation for COnsortias PIpeLIne.
Synthesis in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 201 papers, 31 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
201 citing papers in PubMed, 31 syntheses or guidelines pooled it.
- Genome-wide association studies of infant and toddler temperament in European and multi-ancestry populations.Nature human behaviour · 2026Pooled it
- Genome-wide association analyses of borderline personality disorder identify 11 loci and highlight shared risk with mental and somatic disorders.Nature genetics · 2026Pooled it
- Transforming evidence synthesis: A systematic review of the evolution of automated meta-analysis in the age of AI.Research synthesis methods · 2026Pooled it
- Genome-wide association study of major anxiety disorders in 122,341 European-ancestry cases identifies 58 loci and highlights GABAergic signaling.Nature genetics · 2026Pooled it
- Altered Expression of GABA-Related Genes in Schizophrenia: Insights from Meta-Analyses of Brain and Blood Samples and iPSC-Derived Organoids.Alpha psychiatry · 2026Pooled it
- Multi-ancestry genome-wide association analyses of polycystic ovary syndrome.Nature genetics · 2025Pooled it
- Genome-wide association meta-analysis of age at onset of walking in over 70,000 infants of European ancestry.Nature human behaviour · 2025Pooled it
- Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder.Nature genetics · 2025Pooled it
- Genome-Wide Association Study Meta-Analysis of 9619 Cases With Tic Disorders.Biological psychiatry · 2025Pooled it
- Pooled it
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- Genome-wide meta-analysis of myasthenia gravis uncovers new loci and provides insights into polygenic prediction.Nature communications · 2024Pooled it
- Genome-Wide Association Study of Obsessive-Compulsive Symptoms including 33,943 individuals from the general population.Molecular psychiatry · 2024Pooled it
- The genetic architecture of dog ownership: large-scale genome-wide association study in 97,552 European-ancestry individuals.G3 (Bethesda, Md.) · 2024Pooled it
- Metabolic activity of CYP2C19 and CYP2D6 on antidepressant response from 13 clinical studies using genotype imputation: a meta-analysis.Translational psychiatry · 2024Pooled it
- Multi-ancestry meta-analysis of tobacco use disorder identifies 461 potential risk genes and reveals associations with multiple health outcomes.Nature human behaviour · 2024Pooled it
- Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder.Nature genetics · 2024Pooled it
- Osteoporosis and Primary Biliary Cholangitis: A Trans-ethnic Mendelian Randomization Analysis.Clinical reviews in allergy & immunology · 2024Pooled it
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- Multi-ancestry study of the genetics of problematic alcohol use in over 1 million individuals.Nature medicine · 2023Pooled it
141 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
Abstract
summaryGenome-wide association study (GWAS) analyses, at sufficient sample sizes and power, have successfully revealed biological insights for several complex traits. RICOPILI, an open-sourced Perl-based pipeline was developed to address the challenges of rapidly processing large-scale multi-cohort GWAS studies including quality control (QC), imputation and downstream analyses. The pipeline is computationally efficient with portability to a wide range of high-performance computing environments. RICOPILI was created as the Psychiatric Genomics Consortium pipeline for GWAS and adopted by other users. The pipeline features (i) technical and genomic QC in case-control and trio cohorts, (ii) genome-wide phasing and imputation, (iv) association analysis, (v) meta-analysis, (vi) polygenic risk scoring and (vii) replication analysis. Notably, a major differentiator from other GWAS pipelines, RICOPILI leverages on automated parallelization and cluster job management approaches for rapid production of imputed genome-wide data. A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline. This includes all the associated visualization plots, to allow ease of data interpretation and manuscript preparation. Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work. AVAILABILITY AND IMPLEMENTATION: RICOPILI has a flexible architecture to allow for ongoing development and incorporation of newer available algorithms and is adaptable to various HPC environments (QSUB, BSUB, SLURM and others). Specific links for genomic resources are either directly provided in this paper or via tutorials and external links. The central location hosting scripts and tutorials is found at this URL: https://sites.google.com/a/broadinstitute.org/RICOPILI/home. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.