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RAF_SE columns in the GWAS summary statistic #8
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not sure what you are doing... |
hi gc5k, I have been trying to compute the Fst values with each of three 1KG samples (CEU, FIN, and TSI, respectively) using my GWAS summary statistic: In my statistic file: In reference panel file(1kg_CEU_rsSNP.frq.txt,obtained from demonstration data (https://github.com/gc5k/GEAR/wiki/Fpc): then I perform a command but get an error: -$ java -jar -Xmn7168m -Xms7168m -Xmx7168m gear.jar sfst --meta-batch fst_batch.txt --qt-size fst_batch_N.txt --key SNP EAF EAFSE A1 A2 CHR BP Pval --top 3 --out 2Cohort_sfst GEAR [GEnetic Analysis Repository] [INFO] Subcommand: sfst [INFO] 5 cohorts are remained for analysis. [INFO] Cannot find the p value column in 1kg_CEU_rsSNP.frq.txt [INFO] Cannot find the p value column in 1kg_FIN_rsSNP.frq.txt [INFO] Cannot find the p value column in 1kg_TSI_rsSNP.frq.txt [INFO] Cannot find the se value column in diabetes_Fst.txt I guess it's because there is no SE of EAF columns(sampling variance of EAF,as mentioned in https://github.com/gc5k/GEAR/wiki/Fpc) in my GWAS summary statistics. Should I calculate the sampling variance of EAF in my summary statistic? Thanks! Lee |
It seems that you are engaged in meta-analysis. |
Hi there,
When I try to compute Fst using GEAR, I found there is no RAF_SE columns in my GWAS summary statistics and in 1KG reference panel frq.file.
How can I get RAF_SE columns? Should I sample the GWAS SNPs matched to the 1KG reference samples?
I'm not really sure what is going on. Thank you in advance for your help!
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