Alzheimer’s Disease Neuroimaging Initiative

Question

Question Posted 01/10/18:
Hello,

I am working with ADNI WGS data, which is supplied in aligned bam format. The headers of the bam files state a reference fasta of either 'HumanNCBI37_UCSC_XX.fa' or
'HumanNCBI37_UCSC_XY.fa used. Could you supply these fasta files, or point to where I may download them as there were not supplied on the hard drives provided for the bam files.

Kindest regards,
Roxane

Response posted 01/10/18 by Kwangsik Nho:

for the human reference fasta file, please look at the GATK website (https://software.broadinstitute.org/gatk/).

Response posted 01/16/18 by Roxane Dunbar:

Hi, I've had a brief look, but can't seem to find any particular file that would suggest the two reference files I'm after. Could you be more specific, i.e. the direct link. Or, if the references files were made from combining the individual chromosomes, could you provide details on exactly how this was done so I can identically replicate it.

Many thanks,
Roxane

Response posted 01/16/18 by Kwangsik Nho:

And then, if you look at the header of any vcf file, there is information for the reference.

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