RICOPILI: Rapid Imputation for COnsortias PIpeLIne.

Bioinformatics
Max LamStephan Ripke

Abstract

Genome-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...Continue Reading

References

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Citations

Nov 13, 2019·Translational Psychiatry·Anna E BauerSamantha Meltzer-Brody
Feb 19, 2020·Translational Psychiatry·Shareefa DalvieCaroline M Nievergelt
Nov 13, 2019·Molecular Psychiatry·Andreas J ForstnerJohannes Schumacher
Jul 28, 2020·Translational Psychiatry·Karolina KauppiRolf Adolfsson
Aug 1, 2020·Brain, Behavior, and Immunity·Xiaoqin LiuEsben Agerbo
Apr 13, 2020·The American Journal of Geriatric Psychiatry : Official Journal of the American Association for Geriatric Psychiatry·Najada StringaMartijn Huisman
Jun 11, 2020·Chronic Stress·Frank R WendtRenato Polimanti
Jul 19, 2020·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Saskia P HagenaarsCathryn M Lewis
Aug 21, 2020·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Francesca WaddingtonNina Roth Mota
Oct 24, 2020·The Lancet. Psychiatry·Emma C JohnsonArpana Agrawal
Dec 16, 2020·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Ting LiNina Roth Mota
Jan 20, 2021·Translational Psychiatry·Fotis TsetsosSamuel Zinner
May 9, 2021·American Journal of Human Genetics·Clara AlbiñanaBjarni J Vilhjálmsson
Jun 5, 2021·Translational Psychiatry·Jianhua ChenYongyong Shi
Jun 9, 2021·Biological Psychiatry·Gabriëlla A M BloklandJill M Goldstein
Aug 6, 2021·Molecular Psychiatry·Andreas GötesonMikael Landén
Aug 28, 2021·The World Journal of Biological Psychiatry : the Official Journal of the World Federation of Societies of Biological Psychiatry·V T NguyenS Ripke
Nov 25, 2020··Keijo HeljankoAltti Ilari Maarala

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Methods Mentioned

BETA
genotyping
chip
PCA

Software Mentioned

RIOCPILI
SLURM
rp
R
PLINK
EIGENSTRAT
Perl
GCP Cloud Platform
Google Cloud
bin

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