I have two draft genomes that I would like to compare and I was wondering whether gatk supported such studies?
Thanks for your help!
Most GATK tools (including our variant callers) work by comparing your aligned read data to the reference genome on which the alignment is based. So if you have a reference genome, or can make one of your genomes into a reference genome, then you can use GATK to do this. Otherwise you'll need a different program. But be aware that GATK does not do very well with reference genomes that are composed of many contigs (hundreds to thousands) so if your draft genomes are very fragmented, you will run into memory and performance issues.
It depends a lot on what kinds of comparisons you want to make. The core functionalities of our software are described here: http://www.broadinstitute.org/gatk/guide/best-practices
Thanks for your reply.
I am not working with RNA-seq reads. But what I have is a large number of predicted genes from two closely related species and I was wondering if gatk could identify indels between homologous sequences.