Conversion tool from GEM output to meta-analysis-ready format for CHARGE GLI projects
This python script is used to convert GEM (v1.4.1 or later) output to the meta-analysis-ready format for Phase2 CHARGE Gene-Lifestyle Interactions projects. This version works for python3. There is a version that works for python2 https://github.com/hanchenphd/GEM2CHARGEGLI.
This python script reads GEM Model 1 and Model 2 output files, as well as a SNP info file that includes the imputation flag (Genotyped/Imputed) and quality measure (INFO), and writes the tab-delimited meta-analysis-ready file in gzipped format. Missing values are coded as a period (.), the MAF cut-off is 0.001, and the imputation quality (INFO) cut-off is 0.3.
If GEM was run separately by each chromosome, please only use the Model 1, Model 2 and SNP info file names for chr22. The script assumes files for all other 21 autosomes are located in the same directories respectively (but Model 1, Model 2 and SNP info files can be in different directories), with the same naming convention. It will loop over starting from chr1, so there is no need to specify 66 different input files.
Input files can be gzipped files (.gz).
snpinfofile: SNP info file name. It should at least contain the following information: SNPID, INFO, IMPUTED (see analysis plans). Example: chr22.info.gz (for separate files by each chromosome), or snpinfo.txt (one file for all results).
outfile: Output file name (without .gz). The results will be gzipped. Example: PHASE2.ARIC.AA.HDL.LTST.COMBINED.20220216.txt (the final gzipped output file would be PHASE2.ARIC.AA.HDL.LTST.COMBINED.20220216.txt.gz).
Ename: Variable name for the environmental exposure used in the gene-environment interaction analyses, as shown in your GEM output (NOTE: this is CaSE-senSItiVe). Example: LTST, STST, or ltst, stst.
SNPIDname: SNPID column name in your snpinfofile. Example: SNP.
INFOname: INFO column name in your snpinfofile. Example: Rsq.
IMPUTEDname: IMPUTED column name in your snpinfofile. Example: Genotyped.
snpinfofile_delim: Delimiter in your snpinfofile. Example: tab, space or , (comma).
python GEM2CHARGEGLI_python3.py Phase2.ARIC.AA.HDL.LTST.M1.COMBINED.chr22.out Phase2.ARIC.AA.HDL.LTST.M2.COMBINED.chr22.out chr22.info.gz PHASE2.ARIC.AA.HDL.LTST.COMBINED.20220216.txt LTST SNP Rsq Genotyped tab
The current version is v0.2 (April 21, 2022).
GPL-3.
Please contact Cong Pan (Cong.Pan AT uth.tmc.edu) if you have any questions.
This work was supported by NIH grants R01 HL145025 and R01 HL156991.
If you use GEM in your analysis, please cite
- Westerman KE, Pham DT, Hong L, Chen Y, Sevilla-González M, Sung YJ, Sun YV, Morrison AC, Chen H, Manning AK. (2021) GEM: scalable and flexible gene-environment interaction analysis in millions of samples. Bioinformatics 37(20):3514-3520. PubMed PMID: 34695175. PMCID: PMC8545347. DOI: 10.1093/bioinformatics/btab223.