Date: 201702
Local time of day: 0601-1200
Location: EWR.Airport, NJ
Flight conditions: VMC
Light: Daylight
Aircraft: EMB ERJ 170/175 ER/LR
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Taxi
ATC / advisory: Tower EWR
Reporter organization: Air Carrier
Reporter function: First Officer; Pilot Not Flying
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Training / Qualification
Second reporter function: Pilot Flying; Captain
Anomaly: ATC Issue All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Ground Incursion Runway
Detector: Person Flight Crew; Person Air Traffic Control
When detected: Taxi
Result: Air Traffic Control Issued New Clearance
Contributing factors: Airport; Procedure
Primary problem: Procedure

Narrative: ATIS stated departure runway was 22R at intersection Y (22R/Y) with arrivals landing on 29. Upon taxi out of ramp area; runway assignment was 22L at intersection W (22L/W). Taxi instructions were to taxi via J and make a left hand turn onto S to follow a B737. Upon readback; we were handed off to EWR Tower. Tower cleared us to 'cross 29; right turn Z; and hold short of Runway 22R.'  After clearing 29 and turning on to Z; we were queried by EWR Tower if we can accept a 22R departure from full length. We agreed that we could do so. EWR Tower cleared us to 'Line Up and Wait on Runway 22R.' After scanning the area and performing a Before Takeoff Checklist; we proceeded to complete our turn onto 22R and be aligned with the centerline. Immediately following out alignment with the runway; Tower asked us to hold short of Runway 29. We stopped the airplane immediately and responded that we would.  We were about half of a plane's length into Runway 29.When instructed to Line Up and Wait; there is never any restriction to the pilot to hold short of an intersection. In fact; it has been taught that when you line up on a runway; it is your pavement. In such a rare and unusual instance as this was; EWR Tower should have clearly stated 'Line Up and Wait Runway 22R; hold short Runway 29'


Second narrative: While in line for takeoff for 22L holding short of 22R at Taxiway Z; tower asked if we would be able to take 22R full length for departure. After double checking that we had the appropriate takeoff numbers for 22R we went ahead and put in the new numbers for takeoff. We advised tower that we were good for takeoff for 22R full length. Tower then instructed us to lineup and wait 22R full length. As I was taxing on to the runway I noticed small snow banks to my left restricting me from going onto ZA or going anymore left of the taxiway. I proceeded to taxi into lineup and wait. As I was turning to line up the aircraft with centerline about mid turn tower advised to hold short of 29. I immediately stopped the aircraft. Roughly speaking the nose to the main cabin door were already passed the hold short line for 29. At no point were we advised to hold short of 29 in our clearance to line up and wait.


Synopsis: EMB-170 flight crew reported they were instructed to line up and wait on Runway 22R at EWR from Taxiway Z. During the turn onto Runway 22R they were instructed to hold short of Runway 29 after the nose of the aircraft has already crossed the hold short line.