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

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!

genome alignment variant calling
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written by caroline.c.dickson • caroline.c.dickson

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

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written by JC JC

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