Vatican city itinerary

A half day is the minimum time needed for what you want to do. The Basilica opens earlier than the Museums. There's usually a long line at the Basilica that cannot be avoided by purchasing a ticket, because entrance is free. It is reported the line is much shorter if you get there quite early, so I'd suggest being there no later than opening time (7 AM with, I think, the exception of Wednesdays--but check this), and ideally just a bit earlier so you're in front of the folks who show up at 7 AM. I balked at the prospect of getting up at 5:30 in order to be at the church by 7 AM last year, so I haven't been to St. Peter's recently and cannot estimate how much time you'll want to spend inside. I can only say the line at 3:30 PM or so looked frighteningly long (hundreds and hundreds of people, at least)--though I gather it may move fairly fast.

The Vatican Museums have a separate line for people with reserved entry times (which they convert to tickets once inside). That line is not a problem. The issues are that general admission tickets to the Museums sell out very early, and once you get inside, you are part of a mob. There is no such thing as avoiding crowds in the Vatican Museums; there are only horrible crowds and unbelievable crowds. The Museums have extended their hours this year, opening 1 hour earlier and closing 1 hour later. We hope that means a slight improvement in conditions for visitors, as folks are spread out over more hours. We hope the first entry time (I think 8 AM) will yield a slightly less crowded experience. We imagine late-afternoon times will be a bit less crowded. But to someone visiting for the first time, it will not seem possible that conditions are better in any way. Two hours is probably the rock-bottom minimum time for the Museums unless you simply walk straight to the Sistine Chapel and then back out again. The Sistine Chapel is at the far end of the usual route through the Museums.

As you can see, trying to see the Museums and St. Peters in the same half-day makes it impossible to optimize the experience in both places. It would work better to see the two sights on different days (unless you plan to take a tour as described below). To make it worse, there's quite a long walk between the two entry points, so there's time wasted as you move from the first to the second. The way around that (which usually has worked in the past, but on rare occasions did not) was to sign up for a $$ commercial tour combining the Museums and the Basilica. Those tours (not offered by the Vatican itself) can use a security door to cut between the Sistine Chapel (at the end of the VM tour) and St. Peter's. That avoids having to walk back through the Museums to the exit and around the outside of the building to the door to St. Peter's. But you must stick with the tour group to use that door--no spending extra time in the Museums.

You used to be able to buy those combo tours with Museum entry before the public opening time, but no longer. Some commercial tour operators are still using language that can be interpreted to mean customers get inside the Museums before the public, but that is not accurate (and appears to be intentionally misleading). You are paying for a tour--quite possibly a very good tour, but not for early entry in the sense that you will be alone when you go inside. The Vatican itself sells (less expensive) tours just of the Museums, but they have not in the past allowed tour members to take the back door into St. Peter's.

Tickets for the Vatican Museums can be purchased here: https://tickets.museivaticani.va/home/calendar/visit/Biglietti-Musei

As of today tickets are on sale for visits through April 19, so you'll need to wait a bit to buy yours. But I'd recommend you take a look at all the options to figure out what your preference is.

Thanks acraven.

Based on your post I guess should plan to be at Basilica by 7 and maybe try to reserve 10am slot for the Chapel and the museams.
Is there access to the Sistine Chapel from the Basilica? I understand that I will still have to stand on the line at the entrance to the chapel to clear the security inspite of having reservation.
What happens if I miss the entry at the reserved time due to long lines?
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Is there access to the Sistine Chapel from the Basilica?

There is NO access into the Sistine Chapel without starting at the Museums admission a long walk through the streets around from St Peter's.

I understand that I will still have to stand on the line at the entrance to the chapel to clear the security inspite of having reservation.

NO

You then need the Museums security line - everybody goes through security at both the Museums and at St Peter's - and if you have your ticket already you go in the "have a ticket" line instead of the "buy a ticket" line. You then make your way the full length of the Museums, through many rooms with much to see, in the herd heading to the Sistine Chapel, which is at the completely far end. And then you are there.

What happens if I miss the entry at the reserved time due to long lines?

You need to make allowances so you are not late.

It looks like my best bet is to get the 8am tickets to the Vatican museums, go thru the museum and the Sistine chapel. Exit from the chapel and then stand in line again to enter St. Peter's Basilica which by that time would be pretty long☹. I am planning to do this on friday.
Wish I could split St. Peters and museums into two separate days but I have only 2 full days in Rome and the previous day is marked for the Colosseum, the Forum etc where again one has to go early to beat the crowd.

go thru the museum and the Sistine chapel. Exit from the chapel

you can't exit the museums from the Sistine chapel, unless what you mean is actually going out of the chapel back into the museums. You leave by a different door than you went in, and then you make your way back to the beginning through different rooms of the museums, or of course you can be like a fish swimming upstream and try to see some of those that you walked through on the way in.

When you get back to the entrance area you go out the exit back onto the street, and walk around the outside to the queue for St Peter's, and then clear security and go in.