If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How can I identify SNPs for parentage testing if the offspring is the reference?
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!