0,0,0,DP=1,1,1,1,MQ=2,2,2

0,0,0,DP=1;1;1;1;MQ=2,2,2

sed -r 's/DP.*MQ/n&n/;h;y/,/;/;G;s/.*n(.*)n.*n(.*)n.*n/21/' file

sed -r 's/DP=[^=]*MQ=/n&n/;h;y/,/;/;G;s/.*n(.*)n.*n(.*)n.*n/21/' file

sed -r '/DP=[^=]*MQ=/{s//n&n/;h;y/,/;/;G;s/.*n(.*)n.*n(.*)n.*n/21/}' file

sed -r 's/(.*DP=)(.*)(MQ=.*)/echo -n 1;echo -n 2 |tr "," ";"; echo -n 3/ge' input

kent$  sed -r 's/(.*DP=)(.*)(MQ=.*)/echo -n 1;echo -n 2 |tr "," ";"; echo -n 3/ge' <<<"0,0,0,DP=1,1,1,1,MQ=2,2,2"
0,0,0,DP=1;1;1;1;MQ=2,2,2

awk -F"=" '{gsub(",",";",$2); $1 = $1; print $1"="$2"="$3}' temp.txt

awk -F"=" '{OFS="=";gsub(",",";",$2)}1'

> echo "0,0,0,DP=1,1,1,1,MQ=2,2,2" | awk -F"=" '{OFS="=";gsub(",",";",$2)}1'
0,0,0,DP=1;1;1;1;MQ=2,2,2

perl -plne '$_=~/DP=(.*)MQ/;$a=$1;$a=~s/,/;/g;$_=~s/(.*DP=).*(MQ.*$)/$1$a$2/g'

> echo "0,0,0,DP=1,1,1,1,MQ=2,2,2" | perl -plne '$_=~/DP=(.*)MQ/;$a=$1;$a=~s/,/;/g;$_=~s/(.*DP=).*(MQ.*$)/$1$a$2/g'
0,0,0,DP=1;1;1;1;MQ=2,2,2

perl -F"=" -ane '$F[1]=~s/,/;/g;print join "=",@F'

> echo "0,0,0,DP=1,1,1,1,MQ=2,2,2" | perl -F"=" -ane '$F[1]=~s/,/;/g;print join "=",@F'
0,0,0,DP=1;1;1;1;MQ=2,2,2