I want to know if GATK can do what I want! NGS reads, polyploids, phylogeny

joqbjoqb Posts: 3Member
edited January 2013 in Ask the GATK team

I have 454 reads of loci on polyploid individuals. I am able to produce assemblies containing the different copies of one locus per individual. But I want to extract the reads corresponding to each copies, to then be able to produce phylogenies.
Does the GATK can do something like this?


Post edited by joqb on


  • CarneiroCarneiro Posts: 274Administrator, GATK Dev admin

    You can use the GATK as a framework to develop tools like that, but we do not provide any tools for genome assembly or phylogenies.

    Is your data in a BAM file?

  • joqbjoqb Posts: 3Member

    I don't intend to do the phylogeny through GATK, and I don't have genome data, just a few loci ranging in size between 700 and 2500 bp. I need something using the Linkage Disequilibrium between SNP to produce assemblies containing only one kind of copy.

    Is BAM suitable for assembled reads?

  • CarneiroCarneiro Posts: 274Administrator, GATK Dev admin

    If you need to call SNPs, you can use the GATK (take a look at the best practices document for calling variants).

    With the variants called you can use your favorite program for linkage disequilibrium and phylogeny generation.

  • joqbjoqb Posts: 3Member

    I came to this software because I thought that what you call "haplotype/genotype caller" is what I want to do. Did I mistaken? Could you tell me what these modules do and how the output look like?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,428Administrator, GATK Dev admin

    Hi there,
    To get an overview of the software's capabilities, please read the documentation. You may want to start with the presentation slides from our latest workshop. See the Guide / Events section.

    Geraldine Van der Auwera, PhD

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