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Hi John,

GenomeBrowse can only read VCF files directly that have a specific genomic compression and indexing perform (bgzip) .

If it detects a raw VCF file, it will attempt to write a side-by-side .vcf.gz and .vcf.gz.tbi file on the fly. GenomeBrowse does require write permissions for this step, and for some reason that is not working with your file.

Another solution, is you can run the VCF through the Convert process in the Tools > Manage Data Sources dialog. This converts it to the native annotation track form TSF and puts the file in the annotation user directory, which can then be plotted.