View data in VCF & attach study link

[tria...@connect.hku.hk]

Hi there,

I have two questions about the functionalities of tranSMART, I will be really grateful if someone can help me.

The first question is that, after I have uploaded a VCF file, how can I view the detailed information (like all the id, positions...) in the vcf file? The grid view only tells what sample it is using, and the genome browser show insufficient information about the nodes. As I can check that all the data have been parsed and have been stored in postgresql, I guess there should be a way to view them in tranSMART? Am I right?

A second question, is whether I can attach a link of the source of the study in the study tree? study.params can have study_id, and study_name, so I wonder if it also supports to store a link and display somewhere in the study tree. Now the best I can do is to add an extra link column to the clinical data and let the first data row to write the link in its link column.

Thank you!

[Janneke van der Ploeg]

Hello, 

Which version of tranSMART are you using? Regarding your question about VCF functionality, there have been recent developments in the 17.1 project that improved handling of .VCF files. However, those are mainly back-end changes.

Will ask a colleague to explain further.

For adding metadata to a study, you can use a tags file. This can be provided when uploading clinical data, and allows you to browse metadata via the Dataset explorer by right-clicking on tree nodes. 

More information about uploading tags can be found here: https://github.com/thehyve/transmart-batch/blob/master/docs/data_formats/tags.md

Kind regards,
Janneke Schoots

[tria...@connect.hku.hk]

Hi，

Thank you for your reply.

I am using 16.2 currently. I think the changes you have mentioned are not about the way of displaying data? Currently from my user experience, all the information from .vcf file cannnot be viewed unless download. 

For the tag question, I follow your instructions and try transmart-batch. However, there seems something wrong with gradlew.  For example, ./gradlew capsule will always results in "Exception in thread "main" javax.net.ssl.SSLException: java.security.ProviderException: java.security.InvalidKeyException: EC parameters error".  Do you have any idea with that? Thanks!

Best,

Chen Zihao

[tria...@connect.hku.hk]

Have figure the tag question out. There is something wrong with my old version of java

[Hang PHAN]

Hi, How did you address the java version error? I am running into the same error but after looking through different google indicated sites I couldn't find an answer for it yet. 

Hope to hear back from you

Best

Hang

[Hang PHAN]

Just to give the record for any other who would be in the same trouble as I do, the java version in my path was 1.7, and I had to point the environment variables in my server to java1.8 for the ./gradlew console  command to work. 

Best

Hang