add new attributes

[gybeata]

Hi, First of all thank you for this tool, it looks very promising. My vcf was annotated using VEP with the dbNSFP plugin, and I would like to add all those new custom fields to the data table. I have followed the instructions from here , added a new field, and it appears in the "all attributes field" list on the admin site, however it is not visible on the user interface, so I can not display it in the search results.

Example: Display text: REVEL_score Es name: REVEL_score Path: CSQ_nested

Can you please suggest ? Thank you

[jianxinwang]

Thank you for your interests in using GenESysV. Unless you make you dataset public, you need to create group names and add your users to that group. These items are listed at the top of the admin interface. Please read through the documentation as that saves your time in the long run.

Jianxin

On Thu, Jul 25, 2019 at 10:40 AM gybeata notifications@github.com wrote:

Hi, First of all thank you for this tool, it looks very promising. My vcf was annotated using VEP with the dbNSFP plugin, and I would like to add all those new custom fields to the data table. I have followed the instructions from here https://github.com/ubccr/genesysv/blob/master/docs/source/images/variant_attribute_field.png , added a new field, and it appears in the "all attributes field" list on the admin site, however it is not visible on the user iterface, so I can not display it in the search results.

Can you please suggest ? Thank you

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[gybeata]

Hello, I am not sure I get your answer. Yes, we have created groups and added users to that group. The project in question is accessible by the user, I can do query on the variants and display the default fields, the problem is the custom fields I have added to this particular project (such as REVEL_score), as they are not displaying in the attributes fields. Am I missing something? Thank you, Beata

[jianxinwang]

Not sure what you are missing. Alternatively, you can also hack the two config files (default_vcf_field_gui_mapping.json and default_vcf_gui_config.json) under the config directory to add the extra fields. After modification, rerun the "utils/load_vcf.py" command with "--gui_only" flag.

Jianxin

On Fri, Jul 26, 2019 at 2:52 AM gybeata notifications@github.com wrote:

Hello, I am not sure I get your answer. Yes, we have created groups and added users to that group. The project in question is accessible by the user, I can do query on the variants and display the default fields, the problem is the custom fields I have added to this particular project (such as REVEL_score), as they are not displaying in the attributes fields. Am I missing something? Thank you, Beata

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[jianxinwang]

Hi Beata,

I have another thought. Your new filters/attributes should end up in the "Others" category by default. Have you taken a look at that place? If you still have the same problem, please send us a small section of your VCF file (with header) for testing.

Best,

Jianxin

On Fri, Jul 26, 2019 at 2:52 AM gybeata notifications@github.com wrote:

Hello, I am not sure I get your answer. Yes, we have created groups and added users to that group. The project in question is accessible by the user, I can do query on the variants and display the default fields, the problem is the custom fields I have added to this particular project (such as REVEL_score), as they are not displaying in the attributes fields. Am I missing something? Thank you, Beata

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[jianxinwang]

Hi gybeata,

We identified the cause of the problem you are facing and we are currently working on it. Will update you once we get it fixed. Sorry for the inconvenience.

Jianxin

On Fri, Jul 26, 2019 at 2:52 AM gybeata notifications@github.com wrote:

Hello, I am not sure I get your answer. Yes, we have created groups and added users to that group. The project in question is accessible by the user, I can do query on the variants and display the default fields, the problem is the custom fields I have added to this particular project (such as REVEL_score), as they are not displaying in the attributes fields. Am I missing something? Thank you, Beata

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[jianxinwang]

Hi Beata,

I have updated the code to support the annotations from dbNSFP via the VEP plugin. Please update your code and give it a try. Let me know if you have any questions.

Jason

On Fri, Jul 26, 2019 at 2:52 AM gybeata notifications@github.com wrote:

Hello, I am not sure I get your answer. Yes, we have created groups and added users to that group. The project in question is accessible by the user, I can do query on the variants and display the default fields, the problem is the custom fields I have added to this particular project (such as REVEL_score), as they are not displaying in the attributes fields. Am I missing something? Thank you, Beata

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ubccr/genesysv/issues/2?email_source=notifications&email_token=ACX6JW62ERTEZLJ2LW3P3ELQBKNKXA5CNFSM4IG3MB2KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD23VV7I#issuecomment-515332861, or mute the thread https://github.com/notifications/unsubscribe-auth/ACX6JWYUJ232XPHFSDUXIN3QBKNKXANCNFSM4IG3MB2A .

-- “Study as if you were going to live forever; live as if you were going to die tomorrow.”

                              --Maria Mitchell