When should I use GTFuse?
GTFuse is ideal for extracting dozens or even hundreds of regions (such as medically actionable genes) that are spread out over indexed files (including bams or vcfs).
For extraction of thousands of regions from the same file, the Gene Torrent client should be used instead of GTFuse. That will allow you to download the whole file quickly.
Tools that work well with GTFuse must use the index to jump to the region of the file you want (e.g., samtools view my.bam 2:1234-2345).
Where can I download GTFuse?
Please note that GTFuse is a separate product from the GeneTorrent client that you use to download files from a GNOS repository. If you are interested in purchasing a GTFuse license, please contact us.
Is it possible to mount more than one file at a time?
Yes. You can mount multiple files simultaneously, but we do not recommend mounting more than 10 at a time. Exceeding this number could affect system performance.
Can I use GTFuse with files other than BAMs?
Yes. We designed GTFuse with BAM slicing in mind, but you could mount VCFs or FASTQs, too.
How is GTFuse access authenticated?
GTFuse relies on the same set of GNOS access keys used by the Gene Torrent client. If you don't have an access key to the study where the file is contained, you won't be able to mount the file with GTFuse.
Can I use GTFuse with the IGV browser?
You sure can.
Can I use GTFuse to access files not contained in a GNOS repository?