Question: CALCULATING Z-SCORE from GWAS summary statistics.
0
gravatar for brendaumoh6
6 months 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 • 241 views
ADD COMMENTlink modified 6 months ago by geek_y11k • written 6 months 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 6 months ago by Kevin Blighe66k
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 6 months ago by Kevin Blighe66k • written 6 months ago by brendaumoh60

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

ADD REPLYlink written 6 months ago by geek_y11k
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