neanderthal genome data

Question

[khatami.mahshid]

Hello all,

I wanted to access to a database containing neanderthals genome data, like VCF files exist for the modern human. Does anybody know where can I find it?

thanks a lot

[juanjo75es]

You have here a tool for making homolog searches in the neanderthal genome. It's a new tool I have developed. Iwould like very much to get opinions on its utility and how it could be improved. Please feel free to make any comment directly to my email (it's in the page).

In your case, you can get human genes from Ensembl.org and look for the neanderthal homolog using this tool. The neanderthal genome sequence was downloaded from the Ensembl Neanderthal Genome Browser, which is (I guess) a consensus from different sequences obtained from different neanderthals.

Answer 1

[GenoMax]

BAM files for the neanderthal data aligned against the human genome are available here.

[khatami.mahshid]

what if I wanted VCF files of neanderthals? Because I want to compare neanderthals SNPs with modern human ones.

[GenoMax]

You will find this answer interesting: A: Looking for neanderthal genomes to download

You can find the denosovan VCF files at this link.

[khatami.mahshid]

I have a new question. UCSC has just BAM files for neanderthals. How can I check SNPs in VCF files downloaded from this link with UCSC to make sure the file is correct?