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 get variants only from homozygous region.
I have DNASeq data of an offspring "C" which is cross of parents "A" and "B". Reference genomes of both "A" and "B" are available. I am interested in getting the variants, which should be in the "A" homozygous region. I am confused which reference to use and how to proceed. Your advice will be very valuable. Thank you.