Use openssl to create a PKCS12 file
First create one intcacerts.pem file with your intermediate elements and CA inserted one after another (they must be in PEM format).
Then call openssl
openssl pkcs12 -export -in myservercert.pem -inkey private.key -certfile intcacerts.pem -name "aFriendlyName" -out keyandcerts.p12
(myservercert.pem - PEM, intcacerts.pem CA, , private.key - , )
openssl pkcs12
PKCS12 JKS, -
keytool -importkeystore -srckeystore keyandcerts.p12 -srcstoretype PKCS12 -destkeystore myJKS.jks