Variant Calling for Organism aligned to a reference genome of not the same species

Question

[caroline.c.dickson]

I aligned exon capture data from multiple individuals to a closely related reference genome of my study organism. I was wondering if there is a best pipeline for variant calling under these circumstances. I am looking at GATK, but am wondering if generating gvcf files for all of my samples would be poor practice because they are not the same species as the reference I am using. Any feedback would be great!

[JC]

best pipeline for variant calling under these circumstances

None, you cannot distinguish between intra e inter-species variants.

Maybe it is better to try to assemble your sequenced regions, create a consensus sequence and do variant calling in such areas