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  • rahulvibes
    Junior Member
    • Mar 2010
    • 2
    #1

    Duplicate SNPs

    Dear all,

    I did detection of SNPs from WG re-sequenced data of 25 pigs(~10x). I found out that many SNPs with flanking sequence (200bp) hitting twice or thrice in QTL region. I already did primary filtering on SNPs such as remove SNPs within repeats, set min depth of ref and non-ref allele to 2.

    Now i need to choose SNP for genotyping purpose. is it important to remove all SNPs with multiple hits?

    Welcome any suggestion!!
    Thanks!!

    Regards
    Rahul
    Tags: None
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