Не совсем одна строка:
awk -v 'time=16:13:04,699' -v "date=$(date +%H:%M:%S)" '
function abs(x) {return x<0 ? -x : x}
BEGIN {
split(time, ary, /[:,]/); t_sec = 3600*ary[1] + 60*ary[2] + ary[3]
split(date, ary, /:/); d_sec = 3600*ary[1] + 60*ary[2] + ary[3]
# output difference in minutes
print abs(t_sec - d_sec)/60
}
'