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RICOPILI
Overview
Download & Installation
Preimputation (QC)
PCA
Reference Panels
Imputation
Postimputation
HowTo's
--> Troubleshoot
--> Substeps of each Ricopili Module with default hardware requirements
--> Polygenic Risk Scoring:Ricopili
--> Polygenic Risk Scoring:PLINK
--> LOO-PRS
--> Impute Trios
--> Impute Chr-X from case-control studies
--> Replication/SignTest
--> Replication remeta_repl*.repout.xls columns description.
--> Merge cases & controls from different sources
--> Run the post-imputation module in a different directory
--> Combine seperate imputation directories for meta-analysis
--> Run the post-imputation module on summary statistics
--> Use an external imputation server in combination with Ricopili
--> Build your own reference panel
--> Google cloud Ricopili: Using Ricopili on GCP
--> Formatting summary statistics for S-Predixcan, FUSION and GCTA
FAQ's
FAQs What is a Daner file?
FAQs General
FAQs Installations
FAQs Preimputation (QC)
FAQs PCA
FAQs Imputation
FAQs Trio imputation
FAQs Postimputation
FAQs What kind of data should I expect when using ricopili for PRS?
FAQs refdir_navi
Announcements
Additional Resources
Required Computational Skills
Users Google Group (you need to be member to post, see below)
Developers Google Group
Rare Variant Analysis
Additional Tools
Merge Calling Algorithms
Using Evoker with Broad Data
Version History
Outdated
Installation(Outdated)
External Software and Reference Data (Outdated)
Licensing
RICOPILI
Overview
Download & Installation
Preimputation (QC)
PCA
Reference Panels
Imputation
Postimputation
HowTo's
--> Troubleshoot
--> Substeps of each Ricopili Module with default hardware requirements
--> Polygenic Risk Scoring:Ricopili
--> Polygenic Risk Scoring:PLINK
--> LOO-PRS
--> Impute Trios
--> Impute Chr-X from case-control studies
--> Replication/SignTest
--> Replication remeta_repl*.repout.xls columns description.
--> Merge cases & controls from different sources
--> Run the post-imputation module in a different directory
--> Combine seperate imputation directories for meta-analysis
--> Run the post-imputation module on summary statistics
--> Use an external imputation server in combination with Ricopili
--> Build your own reference panel
--> Google cloud Ricopili: Using Ricopili on GCP
--> Formatting summary statistics for S-Predixcan, FUSION and GCTA
FAQ's
FAQs What is a Daner file?
FAQs General
FAQs Installations
FAQs Preimputation (QC)
FAQs PCA
FAQs Imputation
FAQs Trio imputation
FAQs Postimputation
FAQs What kind of data should I expect when using ricopili for PRS?
FAQs refdir_navi
Announcements
Additional Resources
Required Computational Skills
Users Google Group (you need to be member to post, see below)
Developers Google Group
Rare Variant Analysis
Additional Tools
Merge Calling Algorithms
Using Evoker with Broad Data
Version History
Outdated
Installation(Outdated)
External Software and Reference Data (Outdated)
Licensing
More
Overview
Download & Installation
Preimputation (QC)
PCA
Reference Panels
Imputation
Postimputation
HowTo's
--> Troubleshoot
--> Substeps of each Ricopili Module with default hardware requirements
--> Polygenic Risk Scoring:Ricopili
--> Polygenic Risk Scoring:PLINK
--> LOO-PRS
--> Impute Trios
--> Impute Chr-X from case-control studies
--> Replication/SignTest
--> Replication remeta_repl*.repout.xls columns description.
--> Merge cases & controls from different sources
--> Run the post-imputation module in a different directory
--> Combine seperate imputation directories for meta-analysis
--> Run the post-imputation module on summary statistics
--> Use an external imputation server in combination with Ricopili
--> Build your own reference panel
--> Google cloud Ricopili: Using Ricopili on GCP
--> Formatting summary statistics for S-Predixcan, FUSION and GCTA
FAQ's
FAQs What is a Daner file?
FAQs General
FAQs Installations
FAQs Preimputation (QC)
FAQs PCA
FAQs Imputation
FAQs Trio imputation
FAQs Postimputation
FAQs What kind of data should I expect when using ricopili for PRS?
FAQs refdir_navi
Announcements
Additional Resources
Required Computational Skills
Users Google Group (you need to be member to post, see below)
Developers Google Group
Rare Variant Analysis
Additional Tools
Merge Calling Algorithms
Using Evoker with Broad Data
Version History
Outdated
Installation(Outdated)
External Software and Reference Data (Outdated)
Licensing
Reference Panels
** format changed in summer 2017. I recommend reimputing older imputation runs
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