Broad TCGA Capture kit target intervals

[Jennifer Shelton]

Hello,

I am looking at the target interval list form much of the whole exome sequencing data for the TCGA project from the Broad Institute (BI).

I was wondering about the extremely small interval listed. Many intervals are only 1 bp long for example. These do not represent exons. What are these small and/or intronic intervals.

I am looking in particular at this target bed file:

https://bitbucket.org/cghub/cghub-capture-kit-info/raw/d8b126dd4f33eb7164535e00f0ec9a5985056f34/BI/vendor/Agilent/whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.bed

We are concerned that this will be an issue for tools that process WXS data and expect exons.

Do you maintain any list of the type of target if a variety of target types was included in the WXS experiments?

Thanks,

Jennifer Shelton |  Bioinformatics Programmer
New York Genome Center
101 Avenue of the Americas
New York, NY 10013 
O: (646) 977-7115 
jshe...@nygenome.org

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[Michael Noble]

Dear Jennifer,

The Broad GDAC did not generate sequence data for TCGA.  Please contact the Genomics Platform instead, I think they will be happy to answer your questions.

Best,

-Mike

—

Michael S. Noble

Associate Director for Data Science

Cancer Genome Computational Analysis

The Broad Institute of MIT & Harvard

Manager, Genome Data Analysis Center

The Cancer Genome Atlas

[Jennifer Shelton]

Thanks I will.

Best,

Jennifer Shelton |  Bioinformatics Programmer
New York Genome Center
101 Avenue of the Americas
New York, NY 10013 
O: (646) 977-7115 
jshe...@nygenome.org