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.
Variant calling using a phased genome as reference
I want to do variant calling in a diploid organism using a phased genome as a reference. Therefore, in the reference we have both chromosomes represented. For variant calling with Haplotype Caller should I consider this genome as a diploid (as it is) or a haploid (as the reference has the 2 homolog chromosomes)? What do you think?
Thanks in advance!