Using awk in if statements - if-statement

Question

I have a data file that looks like this:
1 . 0 10109 AA AA
1 . 0 10123 C CCCT
1 . 0 10133 A AAC
1 . 0 10134 A ACAAC
1 . 0 10140 A ACCCTAAC
1 . 0 10143 C CTACT
1 rs144773400 0 10144 T TA
1 . 0 10146 AC A
1 . 0 10147 G C
In the instance of "." in the second column, I would like to replace it with a merged output of columns 1 and 4, like this:
1 1:10109 0 10109 AA AA
1 1:10123 0 10123 C CCCT
1 1:10133 0 10133 A AAC
1 1:10134 0 10134 A ACAAC
1 1:10140 0 10140 A ACCCTAAC
1 1:10143 0 10143 C CTACT
1 rs144773400 0 10144 T TA
1 1:10146 0 10146 AC A
1 1:10147 0 10147 G C
I've been attempting to do this with an if/then statement... but I know I have the syntax wrong, I'm just not sure how wrong.
if [$2 -eq "." /data/pathtofile]
then
awk '{print $1 ":" $4}'
else
awk '{print $2}' >> "/data/cleanfile"
fi
What am I missing?

Answer 1

You could do this through awk itself.
awk -v FS="\t" -v OFS="\t" '$2=="."{$2=$1":"$4}{$1=$1}1' file
OR
$ awk '$2=="."{$2=$1":"$4}{$1=$1}1' file
1 1:10109 0 10109 AA AA
1 1:10123 0 10123 C CCCT
1 1:10133 0 10133 A AAC
1 1:10134 0 10134 A ACAAC
1 1:10140 0 10140 A ACCCTAAC
1 1:10143 0 10143 C CTACT
1 rs144773400 0 10144 T TA
1 1:10146 0 10146 AC A
1 1:10147 0 10147 G C