Fwd: [apollo-dev] cant display vcf

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Fwd: [apollo-dev] cant display vcf

nathandunn




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






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

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

On Tue, Feb 23, 2016 at 9:58 AM, Nathan Dunn <[hidden email]> wrote:




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






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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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

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

2016-02-23 17:17 GMT+01:00 Colin <[hidden email]>:
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

On Tue, Feb 23, 2016 at 9:58 AM, Nathan Dunn <[hidden email]> wrote:




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






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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.








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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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

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

On Tue, Feb 23, 2016 at 11:08 AM, Michel Moser <[hidden email]> wrote:
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

2016-02-23 17:17 GMT+01:00 Colin <[hidden email]>:
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

On Tue, Feb 23, 2016 at 9:58 AM, Nathan Dunn <[hidden email]> wrote:




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






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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.









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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.