Extracting Snps with pvalue <5x10-8 from gwas result
I am working on Multivariate GWAS analysis and I have my results output from the analysis. I would like to extract Snps which have the pvalue < 5x10-8. However,I used
awk '{ if($4 < 5e-8) { print $1 }}' file | head
and
awk '{ if($4 < 0.00000005) { print $1 }}' file | head
This two commands didnt output any data.
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Pierre Lindenbaum
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brendaumoh6 •
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brendaumoh6 •
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with the example your provided above, the following awk script works:
awk '($4<1E-1) {print $1}' input.txt
furthermore: check your LOCALE : https://www.gnu.org/software/gawk/manual/html_node/Locale-influences-conversions.html
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what does the input look like ? show us a few lines.
Above is my dataset
Make sure you have such p-values. Maybe try with
$4<=0.01?Thanks for the input. I used the previous command with another dataset and there was an output. I then sorted my data and discovered that there was no pvalues at that threshold. In conclusion the problem wasnt from the command but rather from the dataset.