Come and share Transmart use cases of VCF files

[oumi...@connect.hku.hk]

Hi guys,

I wonder if Transmart has plugins or analysis workflows for Genomic Data from VCF files. It seems to me that the analysis workflows in Transmart are mainly for the expression array. The Transmart version I am working on is v16.2. 

In this slide, the VCF file can be imported into Transmart and visualized as a track in the Biodalliance Genomic Browser.

http://www.ranchobiosciences.com/wp-content/uploads/2016/01/An-example-of-NGS-workflow-in-tranSMART.pdf

It will be awesome if you guys can provide some use cases of VCF files in Transmart, especially for VCFs from 1000 genome or ExAC.

Suppose there are VCFs under two different studies, is there any plugin in Transmart that can be used to compare them? Like finding the overlap between the VCFs.

Many thanks.

Best,

Min

[Alexander Wait Zaranek]

We would be quite interested in writing a proposal to integrate our
Lightning system (see https://doi.org/10.7287/peerj.preprints.1426v1 )
with i2b2 tranSMART. Would love to further specify the use cases on
this list.

Could you describe your use case in more detail? What performance
goals would you have?

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[Avillach, Paul]

Look at this paper:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172187 

Method 2 is using i2b2/tranSMART to combine VCF with clinical data

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[Ward Weistra - The Hyve]

Hi Min,

Currently the only supported actions with VCF files uploaded in the VCF data format are, as far as I know, to display them on the genome browser for one or two subsets and download them for a subset of subjects.

Best,
Ward

[Avillach, Paul]

Look at this paper:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172187 

Method 2 is using i2b2/tranSMART to combine VCF with clinical data

Online demo with 1000 Genome is here:

https://demo-ngs.hms.harvard.edu

Paul

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[oumi...@connect.hku.hk]

Hi Ward,

Yes. I tried upload VCF file to transmart. Can only display them in genome browser and download.

Thank you very much.

Best,

Min

[oumi...@connect.hku.hk]

Hi Paul,

I read that paper before. I can import VCF into transmart and get the similar folder structure in the paper now.

The Online demo with 1000 Genome is very slow. I cannot open the link. Do you have other similar demo links?

Best,

Min OU

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[Avillach, Paul]

Hi Min

We tested our demo platforms and it works fine

https://demo-ngs.hms.harvard.edu

I was able to reproduce the use case in Fig 3 of the paper

Paul

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