Fwd: glu problem

[Wagner Magalhaes]

---------- Forwarded message ----------
From: Wagner Magalhaes <wcsmag...@gmail.com>
Date: Thu, Apr 19, 2012 at 6:40 PM
Subject: glu
To: "Jacobs, Kevin (NIH/NCI) [C]" <jaco...@mail.nih.gov>

Hi Kevin,

I´m trying to mapping the SNPs from the "HumanOmni1S-8v1_H_SNPlist.txt" from ILLUMINA´s web page but it does not return any SNP, it did well for the EXPRESS. Is there something between them or I´m doing something wrong? GLU did not return any error message.

glu genedb.find_snps -g genedb_hg19_snp131_rtree.db --upbases=0 --downbases=0 ABCB10  --includeloci=HumanOmni1S-8v1_H_SNPlist.txt -o ABCB10_1Ms.txt

Thanks,

Wagner

--

Wagner C. Santos Magalhães, PhD

Phone: +55 31 3409 2572
Lab. Diversidade Genética Humana
Depto - Biologia Geral - Universidade Federal de Minas Gerais

--

Wagner C. Santos Magalhães, PhD

Phone: +55 31 3409 2572
Lab. Diversidade Genética Humana
Depto - Biologia Geral - Universidade Federal de Minas Gerais

[Kevin Jacobs <jacobs@bioinformed.com>]

Hi Wagner,

The problem is that the Omni1S contains variant identifiers that are non-standard and post-date the version of genedb that you are using.  You are also attempting to get hg19/GRCh37 coordinates, which are not the standard annotation provided by Illumina.  

I can certainly generate an updated version of genedb with those annotations, though there are some complexities that have caused me to hold back.  The most serious is that the Omni5 assay uses a different set of annotation for some of the overlapping content that is incompatible with the Omni1S and Omni2.5 hg19 manifests.  My plan was to use annotation with the following precedence order Omni5, Omni2.5, Omni1S, OmniEx, Omni1.

Does that seem sensible to you?

-Kevin

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[Wagner Magalhaes]

Hi Kevin,

On Tue, Apr 24, 2012 at 1:25 PM, Kevin Jacobs <jac...@bioinformed.com> <bioin...@gmail.com> wrote:

Hi Wagner,

The problem is that the Omni1S contains variant identifiers that are non-standard and post-date the version of genedb that you are using.  You are also attempting to get hg19/GRCh37 coordinates,

But they say that on their web site all coordinates are hg19/GRCh37, because that I used the last version you had provided.

 

which are not the standard annotation provided by Illumina.  

I can certainly generate an updated version of genedb with those annotations, though there are some complexities that have caused me to hold back.  The most serious is that the Omni5 assay uses a different set of annotation for some of the overlapping content that is incompatible with the Omni1S and Omni2.5 hg19 manifests.  My plan was to use annotation with the following precedence order Omni5, Omni2.5, Omni1S, OmniEx, Omni1.

Does that seem sensible to you?

Sure, this will great.

Thanks, and sorry for disturb you.

Regards,

Wagner 

[Kevin Jacobs <jacobs@bioinformed.com>]

Hi Wagner,

Illumina has only recently released hg19/GRCh37 versions of their chip manifest files in the last ~6 months, so the vast majority of the world's Infinium data are still using hg18/NCBI 36 coordinates.  Personally, I find hg19 to be more useful, so I'll get started on building a new genedb release with those data.  It will take a few days, but I'll hopefully have something for you shortly.

-Kevin