Implement GWAS catalog SNP tick track

[khadley]

Ayellet attached a table with association details for 8,078 GWAS genome-wide significant SNPs from the NHGRI GWAS catalog for >600 diseases and traits. This is for the GWAS catalog SNP tick track.

Here is a proposed order of summarizing the association info in a box, when clicking on a given SNP tick:

Strongest SNP-risk allele: rs12913832-A Chr position (GRCh37): 15:28365618 Disease/Phenotype: Eye color P-value: 1.00E-300 Odds ratio or beta: 2.49 PUBMEDID: 20585627

Note: A given SNP may be associated with more than one trait. In that case we could list all SNP-trait associations in one box, one below the other with an empty line separating between the associations, as done in the diabetes portal (see attached picture for example).

Here's the accompanying text file information in a private github gist:

https://gist.github.com/khadley/3f8823b278682579d72f

Here's the screen shot.

[jrobinso]

An approximate roadmap.

• [x] decide on a type identifier for the new custom forma. decided. its "gtexGWAS"
• [x] create small example file and put in test / data folder
• [x] extend igv.FeatureParser to handle the new file type by implementing a new decode function. The function should return an object with a minimum of 3 properties: chr, start, end. Look at decodePeak in the file feature/igv.Feature for a model. This function can be passed in to the FeatureParser constructor, but for now just stick it in the file and add a new entry to the switch/case in the constructor.
• [x] write a unit test for the new parser in the test folder. Use testBED.html and testBED.js as a model
• [x] "run" unit test by opening its html in a browser
• [x] you should now be able to create a track using a config option similar to this

{ type : 'gtexGWAS', url 'http://.....', label : 'GWAS track' }

• [x] discuss next step with Jim...

\ NOTE: start position of feature should be in zero based coordinates. For a snp subtract 1 from the value in the file for the start position. The end position == value in the file.

[khadley]

The branch that the changes are on is kane_2April2015_gtexGWAS

[jrobinso]

Kane, how does latest grunt "break build"? I don't want to merge the grunt file "WORKS_LOCAL_BRE..." into master. We need to fix the standard grunt file before the merge. Open a git issue and describe the problem.

On 4/14/15 11:35 AM, khadley wrote:

The branch that the changes are on is kane_2April2015_gtexGWAS

— Reply to this email directly or view it on GitHub https://github.com/broadinstitute/igv-web/issues/65#issuecomment-92913429.

[khadley]

From the git log it looks like Doug added that file and I inherited it when I did a rebase to keep my branch up to date with any changes made in master.

[jrobinso]

Ahh, o.k., I'll delete it then. Should have checked the log, sorry.

On Tue, Apr 14, 2015 at 1:14 PM, khadley notifications@github.com wrote:

From the git log it looks like Doug added that file and I inherited it when I did a rebase to keep my branch up to date with any changes made in master.

— Reply to this email directly or view it on GitHub https://github.com/broadinstitute/igv-web/issues/65#issuecomment-92984986 .

[jrobinso]

Support for basic track is done. Still needs work on popup text, will open a new issue