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I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html

Specifically, the .bam files. I would like to find alignments for neanderthal sequences to human genomes that state ambiguities (such as M or R). However, the data from that site does not have the ambiguities. Is there a way to find such information? Or are there no ambiguity codes in neanderthal alignments?

My goal is to compare diploid neanderthal sequences to diploid human sequences. How do researchers typically deal with this given the limited data they have for neanderthals?

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  • $\begingroup$ Why would you use the draft genome instead of the high coverage Altai genome? $\endgroup$ Jul 27, 2016 at 16:45
  • $\begingroup$ Is there more than 1 whole genome sequence (besides Altai) for neanderthals? I'm looking for at least 5. $\endgroup$
    – ghgh
    Jul 27, 2016 at 18:03
  • $\begingroup$ Oh, ok. There is the Denisova genome (a close relative of Neandertals), but other than that, you really have to stick to low coverage (it was not clear from the question how many genomes you need). But if you use low coverage, you should avoid using Altai or Denisova genomes for the sake of comparability. $\endgroup$ Jul 28, 2016 at 11:25
  • $\begingroup$ Ah ok, thanks. I'm looking for at least 5 or more Neanderthal genomes. I guess I'd have to stick to low coverage then if I want that many. $\endgroup$
    – ghgh
    Jul 28, 2016 at 13:37

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