In the late 90's the first part of a neanderthal genome was decoded. It was done by Svante Paabo and Mathias Kring also, along with a team from Penn STate U , led by M Stoneking. (The Penn STate team actually duplicated the Kring and Paabo study so that they could resolve any issues re: contamination). The teams managed to sequence 380 base pairs of mDNA , . The newest study is apperntly still incomplete as theyve gotta finish the mDNA and the nuclear DNA sequencing.
I think the major finding that seems to discount the "Halfway ape" story is that the no 2 chromosome is seen to be the same "fusing" of 2 chromosomes that differentiate Homo from Pan . (we dont have any way of getting any DNA from Australopithecenes )