emmao
New Member
Posts: 2
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Post by emmao on Apr 26, 2016 12:48:21 GMT
Hello,
I'm an undergrad currently on my professional training year and I'm running a GWAS for my project. I am very new to data analysis and using gcta, I ran a conditional test but it isn't completing.
I've used the command:
gcta64 --bfile cleanfemaleGWAS2 --maf 0.01 --cojo-file femaleSumStats.txt --cojo-actual-geno --cojo-cond rs207565.txt --out Femalegcta
Its been getting to the point:
Reading GWAS summary-level statistics from [FemSumStats.txt] ...
But then stops soon after with the message:
Error in line:
" "
There are 6662 individuals, 529138 SNPs and my summary statistics file is saved as a tab delimited text file, I have checked my summary statistic file for spaces between lines and cant see any. Below is an example of my file:
SNP A1 A2 freq b se p N rs926795 C T 0.1566 1.055 -0.020030423 0.2457 6662 rs2808111 A G 0.199 1.081 -0.021826459 0.1212 6662 rs65420 T C 0.1563 1.084 -0.021527671 0.1037 6662 rs507241 G A 0.1996 0.8991 0.030769748 0.1333 6662
Can someone suggest what might be the problem and how to address it?
Many Thanks
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Post by Jian Yang on Apr 27, 2016 0:07:40 GMT
There should be some unusual data in the file. One suggestion is to read the file in R, check if there are unrecognised data entries by making a few plots and summaries and then save the data to a new file.
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