Sorting of SNPs which has less than 0.05 threshold P-Value

Question

[aarvaBioinfo]

How can we get total number of SNPs in plink association output file as "qassoc" and "adjusted file" which has less than 0.05 P values?

[grant.hovhannisyan]

please post some example lines from that files.

Answer 1

[zx8754]

From the plink manuals the pvalue column for qassoc file is the 9th. So we can use awk to keep the 1st row header, then filter on 9th column value, see example:

awk '(NR==1) || ($9 < 0.05) ' myfile.qassoc > myfile_subset.qassoc

To get the number of rows:

awk '$9 < 0.05' myfile.qassoc | wc -l