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  • meher
    Member
    • Jun 2011
    • 54
    #1

    Ideal params for filtering SNP and Indels

    Hi all,

    Would anyone suggest the criteria to choose ideal GATK and samtools filtering paramters for SNP and Indels(whole exome-sequencing). Is there any particular approach to choose the paramters?

    Any suggestions would be highly appreciated!!!

    Thanks in advance.
    Tags: None
    • Bukowski
      Senior Member
      • Jan 2010
      • 388
      #2
      http://www.broadinstitute.org/gsa/wi...th_the_GATK_v3

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