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Haplotype calling



  • Hilary Miller

    What kind of dataset do you have?  Is it for evaluating CRISPR edits, metagenomic data, or something else?  Do you have a reference sequence?  Are you wanting to incorporate this into a plugin (as this is the plugin development forum)?

  • Ademir Martins

    Dear Hilary,

    Sorry, think I am in a wrong forum.
    I actually have Illumina sequences of a pooled barcoded amplicons.
    I need to recover which haplotypes I find in each library (barcode). 
    What I did was import fastq data do geneious prime, merge the paired files and map them back to a reference sequence. I am doing that for each library. 
    Now I would like to have a list of filtered haplotypes and their frequency in each library

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