Hi there,
I'm developing a workflow to call variants from a dataset of ~600 samples sequenced through genotyping-by-sequencing (GBS) for phylogenomic analyses. My reference genome is rather divergent, around 20 million years. I'm interested in the variants among my sample dataset, not with respect to the reference genome, but those haplotype callers that I'm cheking call the variants with respect the reference (GATK, SAMTOOLS, FreeBayes...) Any suggestion around this problem?
Thanks a lot guys.
I'm developing a workflow to call variants from a dataset of ~600 samples sequenced through genotyping-by-sequencing (GBS) for phylogenomic analyses. My reference genome is rather divergent, around 20 million years. I'm interested in the variants among my sample dataset, not with respect to the reference genome, but those haplotype callers that I'm cheking call the variants with respect the reference (GATK, SAMTOOLS, FreeBayes...) Any suggestion around this problem?
Thanks a lot guys.
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