Saturday, 27 October 2012

Adding Genomic Annotations Using SnpEff and VariantAnnotator - GATK-Forum

http://gatkforums.broadinstitute.org/discussion/comment/1574/#Comment_1574

I am surprised to find this thread recommending only using snpEFF 2.05 (and also ONLY GRCh37.64 ) with GATK. 
snpEFF is now at version 3. I wonder if this recommendation is still true. 


One of my biggest reasons to use snpEff is for the indel annotation and because it's running on java and the process of annotation is pretty fast, it's very amenable to run off my Macbook Pro (or your personal desktop) 


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3 comments:

  1. Anonymous28 August 2013 at 04:16

    The recommendation is still true.

    ReplyDelete
  2. Kevin28 August 2013 at 13:09

    wow ... really? surprised that nothing changed since.
    Do you have any supporting forum post or sth? quite curious why

    ReplyDelete
  3. Anonymous10 September 2013 at 04:20

    http://www.broadinstitute.org/gatk/guide/article?id=50

    Not sure why, they are probably just busy

    ReplyDelete

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