Waltz With Bazir

And from Wikipedia:
http://en.wikipedia.org/wiki/Waltz_with_Bashir

Plot summary

In 1982, Ari Folman was a 19-year-old infantry soldier in the Israel Defense Forces. In 2006, he meets with a friend from his army service period, who tells him of the nightmares connected to his experiences from the Lebanon War. Folman is surprised to find that he does not remember a thing from that period. Later that night he has a vision from the night of the Sabra and Shatila massacre, the reality of which he is unable to tell. In his memory, he and his soldier friends are bathing at night by the seaside in Beirut under the light of flares descending over the city. Folman rushes off to meet another friend from his army service, who advises him to discuss it with other people who were in Beirut at the same time in order to understand what happened there and to revive his own memories. Folman converses with friends, a psychologist and the reporter Ron Ben-Yishai who was in Beirut at the time.

The film ends with animation transitioning to actual footage of the aftermath of the Sabra and Shatila massacre.