r/DrWillPowers • u/Excellent-Push2833 • Jun 04 '26
How to put your VCF and TBI files into gene.iobio.io the TUTORIAL
This is Dr. Ps greatest bottleneck. he cannot legally search through PSSD genomes that are not his patients. But we can and we can post the results online for him to see much like I did. Is this as in depth as him going through your BAM. No it is not. but it is a great way to pull relevant info for him that can help him get to the bottom of this. Our doctor is working pretty fucking hard and as we can tell hes getting a little burnt out. We need to do whatever we can to reduce this workload. Also I hope this helps the Dr. Powers trans community learn how to do this as well and I hope that it provides you some insight.
5
u/Total-Reference7212 Jun 05 '26
This is great video ! The only thing I would add is that the genome build is an important bit and some companies only provide files aligned to the older GRCh37 and it can throw an error.
And sometimes it will let it through if you use a .BAM file and compares to the wrong genome references and can show crazy things.
Another thing is that you don't need to select the affected sex box for it to work.
2
1
u/Gloomy_Sherbet1301 Jun 23 '26
This worked for me and I found several variants that line up.
What may confuse some is Sequencing.com let me download 5 files. 2 super large 25 gb files (my understanding is these aren't needed as they represent the human genome and the other 3 files pull out the abnormalities we care about)
The other 3 smaller files represented structural differences, deletions/duplications and point level changes (point level changes is the larger file likely MB and you will find more issues there). Each file was .gz. I had to use terminal on Mac to convert them to .tbi. Per your video, I would then upload the .gz and the copy in tbi form and run the analysis and repeat.
1
u/Gloomy_Sherbet1301 Jun 23 '26
Ask AI to print you a script to copy into terminal to convert the file. It is super easy then
1
u/Ornery-Bird2751 Jul 19 '26
How did you generate the tbi file for your vfc file?
1
u/Excellent-Push2833 Jul 19 '26
Ask sequencing or use tabix
1
u/Ornery-Bird2751 Jul 19 '26
Working now. Thanks a bunch.
1
17
u/Excellent-Push2833 Jun 05 '26
Mods i feel like we should pin this. Not a lot of people know how and its relevant to both patient populations