[apollo] Fwd: [apollo-dev] cant display vcf

[Nathan Dunn]

Dear apollo users,

I try to visualize a vcf file in webapollo.
I manage to compress the vcf file and index it in tabix.
When i try to load it into webapollo via the File/open window, it recognizes the file automatically.

But when loaded into webapollo, the track appears as a red popup, telling me:

Error
An error was encountered when displaying this track.
Diagnostic message:
404 (Not Found) when attempting to fetch /undefined.tbi

It looks like its not finding the .tbi index.
My naming looks like:

test.vcf.gz
test.vcf.gz.tbi

files were created with:

bgzip -c file.vcf > test.vcf.gz
tabix -p vcf test.vcf.gz

I dont see where i could have gone wrong.

I also dont get any other error messages looking at the terminal where i run the server.

Any ideas?
Thanks, Michel

[Colin]

Hi Michel,
One important thing when you are opening the VCF tabix is to select both
the file.vcf.gz and the file.vcf.gz.tbi in the file upload box


If only the .vcf.gz file is selected, it won't find the tabix index and
give an error like that. I imagine upstream JBrowse could add some better
error messages in this case, but I can reproduce that same error if I only
open the .vcf.gz without the .tbi file

-Colin

Post by Nathan Dunn
Dear apollo users,
I try to visualize a vcf file in webapollo.
I manage to compress the vcf file and index it in tabix.
When i try to load it into webapollo via the File/open window, it
recognizes the file automatically.
Error
An error was encountered when displaying this track.
404 (Not Found) when attempting to fetch /undefined.tbi
It looks like its not finding the .tbi index.
test.vcf.gz
test.vcf.gz.tbi
bgzip -c file.vcf > test.vcf.gz
tabix -p vcf test.vcf.gz
I dont see where i could have gone wrong.
I also dont get any other error messages looking at the terminal where i run the server.
Any ideas?
Thanks, Michel
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[Michel Moser]

Hi Colin,
Thank you, that was exactly the problem.
Do you know if its possible to make SNPs from vcfs draggable into
user-annotations and change the outcome of the anntation?

Would be an awesome feature but probably a bit too fancy =)
Michel

Post by Colin
Hi Michel,
One important thing when you are opening the VCF tabix is to select both
the file.vcf.gz and the file.vcf.gz.tbi in the file upload box
If only the .vcf.gz file is selected, it won't find the tabix index and
give an error like that. I imagine upstream JBrowse could add some better
error messages in this case, but I can reproduce that same error if I only
open the .vcf.gz without the .tbi file
-Colin

Post by Nathan Dunn
Dear apollo users,
I try to visualize a vcf file in webapollo.
I manage to compress the vcf file and index it in tabix.
When i try to load it into webapollo via the File/open window, it
recognizes the file automatically.
Error
An error was encountered when displaying this track.
404 (Not Found) when attempting to fetch /undefined.tbi
It looks like its not finding the .tbi index.
test.vcf.gz
test.vcf.gz.tbi
bgzip -c file.vcf > test.vcf.gz
tabix -p vcf test.vcf.gz
I dont see where i could have gone wrong.
I also dont get any other error messages looking at the terminal where i run the server.
Any ideas?
Thanks, Michel
This list is for the Apollo Annotation Editing Tool. Info at
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

[Colin]

Hi Michel,
That is a great idea. We're actually working on some variant annotation
features in Apollo now, so you can probably expect something like that soon!

We can certainly keep you posted if you're interested in that

-Colin

Post by Michel Moser
Hi Colin,
Thank you, that was exactly the problem.
Do you know if its possible to make SNPs from vcfs draggable into
user-annotations and change the outcome of the anntation?
Would be an awesome feature but probably a bit too fancy =)
Michel

Post by Colin
Hi Michel,
One important thing when you are opening the VCF tabix is to select both
the file.vcf.gz and the file.vcf.gz.tbi in the file upload box
If only the .vcf.gz file is selected, it won't find the tabix index and
give an error like that. I imagine upstream JBrowse could add some better
error messages in this case, but I can reproduce that same error if I only
open the .vcf.gz without the .tbi file
-Colin

Post by Nathan Dunn
Dear apollo users,
I try to visualize a vcf file in webapollo.
I manage to compress the vcf file and index it in tabix.
When i try to load it into webapollo via the File/open window, it
recognizes the file automatically.
Error
An error was encountered when displaying this track.
404 (Not Found) when attempting to fetch /undefined.tbi
It looks like its not finding the .tbi index.
test.vcf.gz
test.vcf.gz.tbi
bgzip -c file.vcf > test.vcf.gz
tabix -p vcf test.vcf.gz
I dont see where i could have gone wrong.
I also dont get any other error messages looking at the terminal where i
run the server.
Any ideas?
Thanks, Michel
This list is for the Apollo Annotation Editing Tool. Info at
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address
with which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.