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!
Question: Variant Calling for Organism aligned to a reference genome of not the same species
5 weeks ago by
caroline.c.dickson • 0 wrote:
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