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  • Compare different files of SNVs

    Dear all,

    I used Bowtie and BWA to align my paired-end reads from Illumina Genome Analyzer to the reference genome. I then used Varscan to call variants. However, the SNVs I get, aren't exactly the same.
    Does anybody know a way to compare both files with SNVs so that I will get a file with SNVs present in both files and then separate files containing the resultant SNVs?

    Thanks a lot!
    Lien

  • #2
    looks like varscan will do this itself using the compare subcommand which is documented to "Merge/intersect/substract 2 sets of variants"

    never tried it myself

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