Give permission user as a site admin in a Site Collection

for that you should be in a farm administrator group of the SharePoint site.  using following stsadmn command you can grant permission to the user.

stsadm –o adduser –url “http://websites/sites/abc”  -userlogin "domain\user"   –useremail  “some@some.com” -username "name" -role "Full Control" -siteadmin