I have a file (file1.vcf) as like this
chr1 254 . A . 80 . . xxxx xxxxx
chr1 255 . T . 80 . . xxxx xxxxx
chr1 554 . G C 80 . . xxxx xxxxx
chr1 554 . A . 80 . . xxxx xxxxx
chr1 754 . G A 80 . . xxxx xxxxx
Based on the fourth and fifth column value I need to create a new file as like this
>file1
ATCAA
It is important that if some value is on fifth column forth one have to replace with that. I tried with following awk and transpose
awk '{if ($5==".") print $4
else print $5}'
but I could able to find a solution for outputting as expected
$ awk '{printf "%s", ($5=="."?$4:$5)}' file
ATCAA
if you need a newline at the end, add END{print ""}