[Gmod-ajax] Block based tracks/LD

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[Gmod-ajax] Block based tracks/LD

Jillian Rowe
Hello all,

I'd really love to see some support for block based tracks, where you
need the entire window space and not a piece for rendering. An example
where the entire window is needed is the LDplot at hapmap 27, and most
heatmap type representations.

I wrote a quick javascript plugin for an LD map using d3 and javascript.
I got the json data by

1. vcftools --gzvcf
/data/share/web_public/jbrowse/1000genomes/chr22/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
--hap-r2 --min-r2 0.5 --ld-window-bp 10000 --out r25.out
2. I also generated some test data shown in the screenshot. Its pos
1-10, all in LD with one another, and a randomly generated r^2 value.
3. From either of these use the attached perl script to generate the
json. This could be easily changed to follow Roberts API for JBrowse
compatible JSON data.
4. The javascript to create the graph uses d3 and is found in the
test.tt2 file.

Will future versions of jbrowse support block based tracks?

Best,
Jillian

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ld.pl (1K) Download Attachment
test.tt2 (5K) Download Attachment
testld.txt.csv (722 bytes) Download Attachment
data.json (6K) Download Attachment
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Re: Block based tracks/LD

Robert Buels-2
On 01/20/2014 03:07 AM, Jillian Rowe wrote:

> I wrote a quick javascript plugin for an LD map using d3 and javascript.
> I got the json data by
>
> 1. vcftools --gzvcf
> /data/share/web_public/jbrowse/1000genomes/chr22/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
> --hap-r2 --min-r2 0.5 --ld-window-bp 10000 --out r25.out
> 2. I also generated some test data shown in the screenshot. Its pos
> 1-10, all in LD with one another, and a randomly generated r^2 value.
> 3. From either of these use the attached perl script to generate the
> json. This could be easily changed to follow Roberts API for JBrowse
> compatible JSON data.
> 4. The javascript to create the graph uses d3 and is found in the
> test.tt2 file.

Cool!  I'll give it a try!

>
> Will future versions of jbrowse support block based tracks?

Yes, support for this is being built into JBrowse 2.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

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Re: Block based tracks/LD

Jillian Rowe
Not sure if I attached the screen shot in the last one.

Here it is. ;)

I'm excited for JBrowse 2!
On 01/20/2014 03:57 PM, Robert Buels wrote:

> On 01/20/2014 03:07 AM, Jillian Rowe wrote:
>> I wrote a quick javascript plugin for an LD map using d3 and javascript.
>> I got the json data by
>>
>> 1. vcftools --gzvcf
>> /data/share/web_public/jbrowse/1000genomes/chr22/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
>>
>> --hap-r2 --min-r2 0.5 --ld-window-bp 10000 --out r25.out
>> 2. I also generated some test data shown in the screenshot. Its pos
>> 1-10, all in LD with one another, and a randomly generated r^2 value.
>> 3. From either of these use the attached perl script to generate the
>> json. This could be easily changed to follow Roberts API for JBrowse
>> compatible JSON data.
>> 4. The javascript to create the graph uses d3 and is found in the
>> test.tt2 file.
>
> Cool!  I'll give it a try!
>
>>
>> Will future versions of jbrowse support block based tracks?
>
> Yes, support for this is being built into JBrowse 2.
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org

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Screenshot from 2014-01-20 11:04:14.png (158K) Download Attachment