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  • Combining pileup and gff3 files

    Hello

    I have one file containing snp calls in a pileup format and another file in gff3 format which contains information of the contigs (exons, introns etc...). I want to summarize where my snps are located, i.e.:

    Contig1 exon1 2snps
    Contig1 intron1, 5snps
    ....

    But I'm having problems writing a script for this. Has anyone had this problem and solved it.

    Cheers,Saemi

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