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Your first command seems to have correct syntax.

$ cat sample5.txt
A|T|X|G
G|X|T|A
G|T|A|X

$ awk 'BEGIN {OFS=FS="|"} {if ($2=="T")sub($1,"T"); print }' sample5.txt
T|T|X|G
G|X|T|A
T|T|A|X

YMMV:
nawk -F, 'FNR==NR{f2[$1]=$2;next} $2+0 in f2 {$3=f2[$2+0]}1' OFS=, file2 file1