CTAT_HumanFusionLib GTEx data format

[Gavin Oliver]

Hi, 

I was wondering if someone could clarify the format of the GTEx data included in the HumanFusionLib.

Here is an example entry:

ZNF76--SAA2     ["GTEx_recurrent_StarF2019"]    {"GTEx_recurrent_StarF2019":"GTEx-Liver:1.143;n=2","ATTS":["GTEx_recurrent_StarF2019"]}

I guess the n=2 refers to the number of samples/individuals the fusion was detected in?  But what about the value 1.143? 

I have done some web searching and perusing of documentation but to no avail.

All insight appreciated!

Best,

Gavin

[Brian Haas]

Hi Gavin,

Here's the complete set of GTEx recurrent fusions we use for annotation:

https://github.com/FusionAnnotator/CTAT_HumanFusionLib/blob/master/fusion_lib_data/data/STARF_Mar2019/GTEx.starF.consolidated.Mar2019.tsv.recurrent.wTissueType.pct_class_n_count

The format is (%_of_samples;n=sample_count)

where the percent of samples corresponds to the percent of samples of that GTEx tissue type.

I generated this a couple years ago w/ an early version of STAR-Fusion (v1.5).  I'll need to update it sometime so it reflects our more current tooling.

best,

~brian

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Brian J. Haas
The Broad Institute
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[Gavin Oliver]

Perfect, Brian.  Thanks for another immediate and helpful responce.

Very much appreciated!

Best,

Gavin

On Friday, May 15, 2020 at 2:15:03 PM UTC-5, Brian Haas wrote:

Hi Gavin,

Here's the complete set of GTEx recurrent fusions we use for annotation:

https://github.com/FusionAnnotator/CTAT_HumanFusionLib/blob/master/fusion_lib_data/data/STARF_Mar2019/GTEx.starF.consolidated.Mar2019.tsv.recurrent.wTissueType.pct_class_n_count

The format is (%_of_samples;n=sample_count)

where the percent of samples corresponds to the percent of samples of that GTEx tissue type.

I generated this a couple years ago w/ an early version of STAR-Fusion (v1.5).  I'll need to update it sometime so it reflects our more current tooling.

best,

~brian

On Fri, May 15, 2020 at 1:57 PM Gavin Oliver <gavin...@gmail.com> wrote:

Hi, 

I was wondering if someone could clarify the format of the GTEx data included in the HumanFusionLib.

Here is an example entry:

ZNF76--SAA2     ["GTEx_recurrent_StarF2019"]    {"GTEx_recurrent_StarF2019":"GTEx-Liver:1.143;n=2","ATTS":["GTEx_recurrent_StarF2019"]}

I guess the n=2 refers to the number of samples/individuals the fusion was detected in?  But what about the value 1.143? 

I have done some web searching and perusing of documentation but to no avail.

All insight appreciated!

Best,

Gavin

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