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Post by gat2010 on Feb 15, 2021 8:53:35 GMT
Dear all, I am trying to run GCTA with SBLUP option: gcta64 --bfile ../1000G_EUR --cojo-file ../BMI_GWAS_All_ancestry.txt --cojo-sblup 6.69e6 --cojo-wind 1000 --thread-num 20 --out BMI. The summary statistics used here are from GIANT study for BMI. In the output file: 1:1865298:A:G A -0.0153 -nan 1:1873453:A:G G -0.0153 -nan 1:1873514:A:G A -0.0153 -nan 1:1873525:C:T T -0.0153 -nan 1:1873625:A:G A -0.0164 -nan 1:1874581:A:G A -0.0037 -nan 1:1875145:C:T C -0.0036 -nan 1:1875267:A:G A -0.0037 -nan 1:1888193:A:C A -0.0131 -nan 1:1888369:A:G A -0.0066 -nan 1:1892325:C:T T 0.0004 -nan 1:1916587:G:T T -0.0007 -nan 1:1987762:C:T T -0.0017 -nan 1:2024064:C:T T 0.0002 -nan 1:2026361:A:G A -0.0045 -nan 1:2026749:A:G G 0.0001 -nan Most weights are -nan. The tool ran completely without any error. I am looking in the log file that states “Phenotypic variance estimated from summary statistics of all 2100301 SNPs: 1.56224 (variance of logit for case-control studies)”. However, the GWAS was conducted on a quantitative trait (BMI). I looked on the tool website, but didn’t find any option to change this assumption of trait. Could you please help in resolving the two issues, I am hopeful that these two issues are interconnected. Thank you once again for your help. Regards Gaurav
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