CHARGE-GLI Material
EasyQC2 (CHARGE-GLI: Quality control and file cleaning)
Description
EasyQC2 is an extension of the previous EasyQC R-package that provides advanced and improved functionality.
Download
Current Version: https://github.com/winkusch/Easy2 (externer Link, öffnet neues Fenster)
Please use the R package Easy2 from github, which includes the latest updates.
Easy2 contains all EasyQC2 functionality and is compatible with the ecf-scripts from below.
CHARGE Gene-Lifestyle Interaction working group - Cleaning
The following EasyQC2 scripts and reference data were used for quality control of study-specific gene-environment (GxE) interaction GWAS within the CHARGE Gene-Lifestyle Interaction working group. The GxE Interaction GWAS were conducted using LinGxEScanR (externer Link, öffnet neues Fenster), GEM (externer Link, öffnet neues Fenster) or MMAP (externer Link, öffnet neues Fenster).
Step 1: Study-QC
Script:
charge2qc_240424.ecf (externer Link, öffnet neues Fenster) (for binary E)
charge2qc_quante_240424.ecf (externer Link, öffnet neues Fenster) (for quantitative E)
The script is capable with raw LinGxEScanR, GEM and MMAP output. It will conduct study-level QC and create CLEANED files. The script should be run for each study separately. Further details and instructions on the individual steps are shown as comments in the script. The script requires liftover and allele-frequency reference files that are described in the following.
Script to check joint 2df P values:
charge2checkp_221221.ecf (externer Link, öffnet neues Fenster)
This script compares joint 2df P values calculated from the given summary statistics (beta_g, se_g, beta_gxe, se_gxe and covariance) with the given joint 2df P values. NOTE: The current version of the Study-QC script ("221221" version above) already contains these checks. You must only run the checkp script if you have cleaned the data with an earlier version of the Study-QC script.
Liftover reference:
1000G_p3v5.TOPMed_Imputed.add_UKB.Liftover_hg19to38.txt.gz (externer Link, öffnet neues Fenster)
The liftover reference file contains hg19 and respective hg38 chromosomal positions for 76,553,613 genetic variants. The variants included were obtained from an imputation of 1000 Genomes reference files to TOPmed (as described below) and from the imputed UK Biobank data (available through approved UK Biobank research project #8343 (externer Link, öffnet neues Fenster)).
Allele frequency references:
1000G_AFR_p3v5.TOPMed_Imputed.Allele_Freq.hg38.txt.gz (externer Link, öffnet neues Fenster)
1000G_AMR_p3v5.TOPMed_Imputed.Allele_Freq.hg38.txt.gz (externer Link, öffnet neues Fenster)
1000G_EUR_p3v5.TOPMed_Imputed.Allele_Freq.hg38.txt.gz (externer Link, öffnet neues Fenster)
1000G_EAS_p3v5.TOPMed_Imputed.Allele_Freq.hg38.txt.gz (externer Link, öffnet neues Fenster)
1000G_SAS_p3v5.TOPMed_Imputed.Allele_Freq.hg38.txt.gz (externer Link, öffnet neues Fenster)
The ancestry-specific allele frequency reference files contain three columns:
(i) 'cpaid' : Marker identifier using the format chr:pos:A1_A2 with A1 and A2 in alphabetical order and chr/pos on hg38
(ii) 'AA1_Freq': allele frequency of A1 for the respective ancestry
(iii) 'R2': Imputation quality for the respective ancestry
The allele frequency reference files were derived through imputation of ancestry-specific 1000 Genomes p3v5 reference files to TOPmed using the TOPmed imputation server (externer Link, öffnet neues Fenster). The imputation was conducted and results kindly provided by Michael Brown (öffnet Ihr E-Mail-Programm) from the University of Texas Health Science Center at Houston.
Step 2: Premeta-QC
Script:
charge2premetaqc_231214.ecf (externer Link, öffnet neues Fenster) (for binary E)
charge2premetaqc_quante_231214.ecf (externer Link, öffnet neues Fenster) (for quantitative E)
The script is capable with CLEANED study files from step 1. It performs a range of QC checks across studies and should be run with multiple studies at once. Further details and instructions on the individual steps are shown as comments in the script.
Requirements
R 3.1.0 or higher.
Only UNIX/LINUX systems are supported.
Citation
If you use EasyQC2/Easy2 please cite
"Winkler et al.: Quality control and conduct of genome-wide association meta-analyses. Nature Protocols 2014"
and (if possible) reference our webpage "www.genepi-regensburg.de/easyqc2".
Thank you.
License
EasyQC2 is licensed under the GNU General Public License, version 3.
Copyright © 2022 by Thomas Winkler.
Although we hope that EasyQ2C will be useful, it is published WITHOUT ANY WARRANTY.
Contact
If you require support for a different platform or have any further questions please e-mail thomas.winkler(at)ur.de
EasyStrata2 (CHARGE-GLI: Analytical framework)
Description
EasyStrata2 is an extension of the previous EasyStrata R-package that provides advanced and improved functionality.
CHARGE GLI - Analytical framework
You can download the latest material required to run all analyses from CHARGE-GLI analytical framework here: CHARGE-GLI (externer Link, öffnet neues Fenster).
Current Version of R package: https://github.com/winkusch/Easy2 (externer Link, öffnet neues Fenster)
Please use the R package Easy2 from github, which includes the latest updates.
Easy2 contains all EasyStrata2 functionality and is compatible with the ecf-scripts from below.
Requirements
R 3.1.0 or higher.
Only UNIX/LINUX systems are supported.
Citation
If you use EasyStrata2 please cite
"Winkler et al.: EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data. Bioinformatics 2015".
Thank you.
License
EasyStrata2 is licensed under the GNU General Public License, version 3.
Copyright © 2023 by Thomas Winkler.
Although we hope that EasyStrata2 will be useful, it is published WITHOUT ANY WARRANTY.
Contact
If you require support for a different platform or have any further questions please e-mail thomas.winkler(at)ur.de