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

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!

RNA-Seq R genome gatk galaxy • 121 views
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