[GET-dev] where do I get raw data ?

[Madeleine Price Ball]

Sorry, it's been changing as we update the genome analysis methods.

If you click on any of the PGP genomes that say "with indel and
coverage" it should have indel and coverage information in the
downloadable gff data. For example:

http://evidence.personalgenomes.org/genomes.php?display_genome_id=65711e3d6829f08c2f8aeeaf06b67b4d2c744e38

If you click on "Source data: download GFF (115 MB)" you'll get a file
called "PGP1_\(George_Church\)_with_indel_and_coverage.gff" but ...
it's actually gzipped. Sorry. You'll probably want to do:

mv PGP1_\(George_Church\)_with_indel_and_coverage.gff
PGP1_\(George_Church\)_with_indel_and_coverage.gff.gz

FWIW - there's a fix for this bug here, maybe Tom can pull it to the main site:
https://github.com/madprime/get-evidence/commit/129e510318bd5381d86cd6ab1e9aca5976bd1c46

I've made a write up for how indels and coverage are marked here:
http://evidence.personalgenomes.org/guide_upload_and_source_file_formats

On Tue, Dec 21, 2010 at 8:43 AM, Leon Peshkin <peshkin at gmail.com> wrote:
> Hello!
>
> Could someone help me with a pointer to PGP-10 raw data files, that is more
> than list of SNPs.
> I am interested to get a pretty short (few thousand nucleotide) chunks to
> compare across individuals,
> but it might contain deletetions in some.
>  Sasha mentioned that data is available from
> http://evidence.personalgenomes.org/genomes
> but I do not see any mention of "coverage and indels" at the page.
> There is a link to http://evidence.personalgenomes.org/download
>  which is linked to the SQL dump and flat tsv file, but not BAM or SAM, so I
> am somewhat confused.
>
> -Leon
>
>
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