Non-human reference genome for GATK SV Pipeline

Hi,

I am interested in running the GATK SV pipeline of protistan genomes. I have two reference genomes representing strains of the alga I am working with. I would like to compare references to  Illumina sequences of the genomes of substrains of varying phenotypes. Please let me know if it is possible to run the aforementioned pipeline with my samples. Thanks!

Chris Whelan Mark Walker Samantha (she/her)

https://app.terra.bio/#workspaces/help-gatk/GATK-Structural-Variants-Single-Sample