Question: CALCULATING Z-SCORE from GWAS summary statistics.
0
gravatar for brendaumoh6
12 weeks ago by
brendaumoh60 wrote:

How do I calculate Z-score from a GWAS summary statistics. Note; I tried using awk command but i got an error massage :

awk '{print $0, $3/$4}' SBP_gwas.txt > SBP_Zscore
awk: cmd. line:1: (FILENAME=SBP_gwas.txt FNR=1) fatal: division by zero attempted
z score • 144 views
ADD COMMENTlink modified 12 weeks ago by geek_y11k • written 12 weeks ago by brendaumoh60
1

Please show a sample of your input data. Also, it seems that you are simply trying to divide column #3 by #4?

I have put some code here for calculating Z-score from GWAS output: A: SNP dataset and Z Score

ADD REPLYlink written 12 weeks ago by Kevin Blighe61k
snpid beta_uganda se_uganda beta_DCC se_DCC beta_DDS se_DDS beta_AADM se_AADM studyno pval_fe beta_fe se_fe pval_re beta_re se_re pval_re2 Isquare Q pval_Q tau_square pval_uganda pval_DCC pval_DDS pval_AADM af_uganda af_DCC af_DDS af_AADM no_uganda no_DCC no_DDS no_AADM
10:100000012:G:A -1.251398e-01 5.619498e-02 -1.066799e-01 9.506664e-02 2.889494e-02 1.168009e-01 -0.05826 0.06943 4 0.0210307 -0.0867148 0.0375806 0.0210307 -0.0867148 0.0375806 0.0280165 0.00000 1.65933 0.646013 0.00000 0.0259549 0.261795 0.804609 0.401403 0.972764 0.960781 0.965522 0.97619 6395 1478 1117 4623
10:10000010:C:T NA NA NA NA NA NA -0.05957 0.1432 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.677416 NA 0.999313 0.999545 0.994505 6395 1478 1117 4623
ADD REPLYlink modified 12 weeks ago by Kevin Blighe61k • written 12 weeks ago by brendaumoh60

So, given your input file, you could not spot why there is an error in your awk?

ADD REPLYlink written 12 weeks ago by geek_y11k
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