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  • bioits
    Member
    • Aug 2010
    • 23
    #1

    New to ILMN platform and have couple questions on on VCF filtering

    Got a few VCF files, which have over 15K variants (rows) in each VCF file. I'd like to filter down reasonable number of rows before doing further analysis. While checking filter option, I only got less than 20 rows with "pass". Is it normal range of passed variants in general or the sequencing quality got really messed up? In this case, should I apply less stringent filters?
    Thanks
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