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How can I identify SNPs for parentage testing if the offspring is the reference?

henriettevdzhenriettevdz South Africa Member

Hi everyone!

I'm developing a SNP parentage verification panel. I've de novo sequenced and assembled the genome of the offspring and this is my reference genome. I have also sequenced the genomes of both the parents at a lower coverage. I now want to map the parents' reads against the reference. However what I have now realized is that the reference will only have one nucleotide at a position. So I will need to identify positions where one parent is a homozygote for a nucleotide and the other parent is also a homozygote but for another nucleotide at that position and therefore the offspring will be a heterozygote but it will show as only one of the two nucleotides on the reference genome.

Is there perhaps any tools available to identify SNPs in this way?

Thanks a lot!

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @henriettevdz,

    To do this correctly you would need a graph-based representation of the reference genome, and tools that would handle that (which GATK tools don't). Is there a reason why you're basing your analysis on using the offspring assembly as reference? Is this non-human data?

    Ideally you would want to use a reference that is representative of your organism overal (eg based on a population) then do joint variant calling of all three samples against that reference. Then you can compare the calls and perform whatever computation you want to do to ascertain parentage. I expect there are tools that can do this, i.e. infer parentage based on variant calls made on trios, though I'm not personally familiar with any particular program.

  • henriettevdzhenriettevdz South Africa Member

    Hi Geraldine!

    Thanks for your answer!

    Yes it is for a bird species - lovebirds - which are bred as pets. We did the genome assembly first. What my plan is, is to first identify SNPs in the one family because they are rather inbred. If I can identify variants in this family where both parents are related, then the likelihood that the SNPs will be found in the broader population is high. So I want to identify around 200 SNPs and then test these back in the broader population of birds that are from different aviaries and even wild types (these birds are still found in the wild).

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