How can I analyze a VCF dataset without an annotated reference genome

Question

[julianneradford]

Hi there,

I am trying to compare genomic variation across 8 transcriptome libraries. I have cleaned up the data, mapped it with BWA, marked duplicates, sorted the BAM, used FreeBayes to make the VCF files. However, I do not have an annotated reference genome for the species (Reticulitermes flavipes), I only have a reference transcriptome. Is there any way I can meaningfully analyze the VCF files and visualize the variants across the different populations without an annotated reference?

Thank you!