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  • christophpale
    Member
    • May 2010
    • 16
    #1

    Good variant filters

    Hi,
    So I have finally managed to get GATK 1.3 to spit out indels and snps for my exome data. Can someone please share the filters that are reliable. I am hoping to get ti/tv ~ 3.0 and proportion of snps in dbsnp to be ~91% in the targetted coding region. It would be great to see what different people use and what validation success rate they are achieving.
    thanks
    Tags: None
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