VTP pruning is an automated process - a switch can prune off VLANs that it doesn't need, and automatically re-add them should access to the 'pruned' VLANs be needed. Manual clearing of VLANs from a trunk is hard-coding what VLANs are and are not allowed on a trunk.
Obviously VTP Pruning needs a VTP domain to be established and pruning enabled within the Domain.....
Switchport trunk allowed specifies which VLANs are allowed on the trunk. This is one of the commands you can use to manually remove (prune) VLANs from a trunk link. By default all VLANs are allowed on the link and specifying them using this command only allows those that are listed.
Note: If you use this command, then it will allow only the vlans specified when you issue the command. For example if you wanted to allow only VLAN 10,20, and 30, you would enter the command:
switchport trunk allowed vlan 10,20,30
If later you wanted to add vlan 40 you would have to enter the command:
switchport trunk allowed vlan 10,20,30,40
switchport trunk allowed vlan add 40
If you entered: switchport trunk allowed vlan 40, then that would be all that is allowed. See the following link for more details:
The switchport trunk pruning vlan command specifies which VLANs are allowed to be pruned, by VTP pruning. Whatever you enter after this command is added to the prune list, which is all VLAN's by default. This command is useful when you don't want to prune a particular. For example let's say you had a VLAN that you never wanted VTP to prune, then you could remove that VLAN from the prune list with the command switchport trunk pruning vlan remove xxx.
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