Does gatk support genome comparison studies?

SheaphSheaph IrelandPosts: 2Member

Hi,

I have two draft genomes that I would like to compare and I was wondering whether gatk supported such studies?

Thanks for your help!

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  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,365Administrator, GATK Developer admin

    Hi there,

    It depends a lot on what kinds of comparisons you want to make. The core functionalities of our software are described here: http://www.broadinstitute.org/gatk/guide/best-practices

    Geraldine Van der Auwera, PhD

  • SheaphSheaph IrelandPosts: 2Member

    Hi Geraldine,

    Thanks for your reply.
    I am not working with RNA-seq reads. But what I have is a large number of predicted genes from two closely related species and I was wondering if gatk could identify indels between homologous sequences.

    Regards
    Stephen

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