http://www.techonia.com/create-vlan-on-linux-with-cisco-catalyst-switch

Linux side

We will use eth1 interface in the Linux box. We have to bring the interface up without IP address assigned to it before we can use it.

ifconfig eth1 0.0.0.0 up

We will create interface vlan 11 and vlan 12 on this eth1 interface. To create a vlan interface, use ‘vconfig add’ command as below:

vconfig add eth1 11
Added VLAN with VID == 11 to IF -:eth1:-
 
vconfig add eth1 12
Added VLAN with VID == 12 to IF -:eth1:-

ifconfig eth1.11 192.168.11.254 netmask 255.255.255.0 up
ifconfig eth1.12 192.168.12.254 netmask 255.255.255.0 up

Cisco side

http://www.samuraj-cz.com/clanek/cisco-ios-7-konfigurace-vlan-vtp/

switch(config)#int f0/16
switch(config-if)#description Trunk_To_Linux_Router
switch(config-if)#switchport trunk allowed vlan 11,12
switch(config-if)#switchport mode trunk
switch(config-if)#no shutdown
switch(config-if)#exit