AA   762    8640    BB    CC     DD      EE=T;FF=C;GG=G;HHA
II   852    6547    JJ    KK     LL      MM=G;NN=P;QQ=RF

AA   762    8640    BB    CC     DD      EE=T    FF=C    GG=G   HHA
II   852    6547    JJ    KK     LL      MM=G    NN=P    QQ=RF

awk 'BEGIN { FS=";" } { print $1, $2, $3}' file

awk 'BEGIN { FS=";" } { print $0}' file

awk -F'[[:space:];]' -vOFS='t' '{$1=$1;print}' input.txt
AA  762 8640    BB  CC  DD  EE=T    FF=C    GG=G    HHA
II  852 6547    JJ  KK  LL  MM=G    NN=P    QQ=RF

awk 'BEGIN{FS=OFS="t"}{gsub(/;/,"t",$NF)}1' file

$ cat file
AA  762 8640    BB  CC  DD  EE=T;FF=C;GG=G;HHA
II  852 6547    JJ  KK  LL  MM=G;NN=P;QQ=RF

$ awk 'BEGIN{FS=OFS="t"}{gsub(/;/,"t",$NF)}1' file
AA  762 8640    BB  CC  DD  EE=T    FF=C    GG=G    HHA
II  852 6547    JJ  KK  LL  MM=G    NN=P    QQ=RF

tr ";" "t" <yourfile