I have the G12 (nozzle cleaning) enabled in Marlin. Is there a way that I can call this command in Slicer3r just before the print begins.
Ie after the nozzle has heated ?

Putting in under Printer settings -> Custom gcode > start gcode is before heating takes place.

Thanks

If there are any heating commands in the custom start gcode Slic3r won't put them in by itself. So you can do something like

M109 S[first_layer_temperature_0] ; heat up nozzle
G12 ; clean nozzle

in your startup code so you can get the behavior you want. I use this on my printer so the bed heats up before I home (I use an inductive sensor in the middle of the bed so I want the bed to do any warping before probing). The relevant section of my start gcode looks like this:

M190 S[first_layer_bed_temperature]
G4 S30 ; Wait for bed temperature to stabilize
G28 ; home all axes
M420 L0 ; Load UBL matrix
M420 S1 ; Activate UBL
M420 Z10.0 ; 10mm fade height

G0 F6000 X40 Y-5 Z0.5 ; Somewhere ooze isn't a problem
M109 S[first_layer_temperature]
M150 R255 B255 U255 W255 ; Let there be light!
; Extrude a bit so we end up knocking it off with the edge of the bed
M83  ;Extruder relative
G0 F200 E7.5 ; Extrude a bit (should end up extruding about 15cm with a 0.4 nozzle)
G0 E-0-.5; retract