Is anyone aware of a recent comparison of various variant callers (GATK, FreeBayes, etc) for non-model organisms, please? There are many out there for human data, obviously because there are good reference sets. My data is hundreds of whole genomes from an insect species (>10% sites variable!), and we traditionally use GATK. However, the GATK HaplotypeCaller is rather slow for this data. Sensitivity is a higher concern than precision (not looking for specific SNP associations).