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Haplotype calling

Is there a way to have a list of haplotypes (and frequency) [identical sequences] extracted from an amplicon Illumina sequencing data?

Thank you

Ademir Martins

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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)?

Hilary Miller 0 votes
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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
Ademir Martins 0 votes
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