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?
From the plink manuals the pvalue column for [qassoc file][1] 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

  [1]: https://www.cog-genomics.org/plink2/formats#qassoc