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  • How to analysis with allotetraploid genome

    Hi
    I recently got SNP analysis of allotetraploid genome(AADD genome type)
    My steps are
    Fastqc
    trimming
    next is mapping onto reference genome
    My concern is with homoelogous region how should i tackle this whjile mapping?
    Is there quality filtering parameter which can tackle homoelogous region and give true SNPs and Indels
    Also what are concern should i put while doing QC and trimming?

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