A script to parse a RAD tags file and display the line number and individual id/tag id pairs field when the field has only a specific number of individuals (in the case n==3)

parse_rad_tags.awk

BEGIN {
  FS="\t"
}
{
	lena=split($9,a,",")
	for (i=1;i<=lena;i++) {
		split(a[i],b,"_")
		freq[NR][b[1]]++
	}
}
END {
	for (j in freq) {
		n=0
		for (k in freq[j])
			n++;
		if (n == 3)
			print NR, ":", $9
	}
}