A question about pancan_mutation_blacklist.v14.hg19.txt

Wei Zhang

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Apr 25, 2016, 9:53:49 PM4/25/16

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Dear Sir/Madam,

I'm currently looking into mutsigCV results from Firehose. I noticed the genes are filtered by pancan_mutation_blacklist.v14.hg19.tx. May I ask for the criteria of this blacklist? And could you please let me know where can I download it? Thanks!

Best regards,

Wei

--

Wei Zhang PhD
Trey Ideker lab
University of California, San Diego
Department of Medicine
Biomedical Research Facility 2 (BRF2), Room 3A16
9500 Gilman Drive
La Jolla, CA 92093

David Heiman

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Apr 26, 2016, 11:10:16 AM4/26/16

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Hi Wei,

My understanding of the blacklist is that it is used to filter out recurrent mutation sites that the MutSig development team found to cause issues with the determination of significance. Because these by nature include germline mutations that may not have been part of available databases at the original generation of the MAF, we are not permitted to release it to the public.

I will forward your question along to the developers to see if they can lend any more clarity.

Regards,

David

--

David Heiman

Run Operations Engineer

TCGA Genome Data Analysis Center

The Broad Institute of MIT and Harvard

415 Main Street

Cambridge, MA 02142

more...@gmail.com

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Sep 16, 2016, 11:20:08 AM9/16/16

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Dear Wei and David,

I would also appreciate it if you could tell me how I can download this blacklist file.

Many Thanks,

Carlos S. Moreno, PhD

Associate Professor
Department of Pathology & Laboratory Medicine
Department of Biomedical Informatics
Winship Cancer Institute of Emory University
Emory University School of Medicine

On Monday, April 25, 2016 at 9:53:49 PM UTC-4, Wei Zhang wrote:

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