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  • lre1234
    Senior Member
    • Aug 2011
    • 110
    #1

    SNP/Indel filtering

    Hi all,
    I am trying to filter a set of SNPs and indels that I have found. Essentially, I would like to find a way to remove an groupings of SNPs which fall into small windows of sequence. So for example, if I have 3 SNPs/indels which are all located within say 10ps of each other, I would like to remove these. In particular, I would like to do this for Indels. Is there a simple way of doing this. It seems like the GATK variantFiltration --clusterWindowSize would do this, but I am not sure.
    Any advice would be helpful.
    Thanks
    Tags: filtering, snp analysis
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