Extending references

[vrockai]

While the hg18 and hg19 references are supported by default, is there any plan to support more references? I'm interested in grch38/hg20 in particular.

The desktop IGV browser can accept a .genome file, like: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome

Is this file type somehow supported in IGV.js, too? What are my options if I want to use hg20 with IGV.js?

[ttriche]

hg20 doesn't exist... the hg38 genome file you pointed at is the one you would want for the-assembly-that-followed-hg19. In other words, hg38 is a 0-indexed version of GRCh38, but the sequences on each chromosome are (should be) the same.

I can't find a live demo using the hg38 reference but this problem was referred to and (apparently) solved in #315.

--t

On Fri, May 5, 2017 at 9:12 AM, Viliam Rockai notifications@github.com wrote:

While the hg18 and hg19 references are supported by default, is there any plan to support more references? I'm interested in grch38/hg20 in particular.

The desktop IGV browser can accept a .genome file, like: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome

Is this file type somehow supported in IGV.js, too? What are my options if I want to use hg20 with IGV.js?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/363, or mute the thread https://github.com/notifications/unsubscribe-auth/AAARIoQPQTxLmLVatqyv9JaJ3q4lkQnuks5r20p7gaJpZM4NSHy7 .

[jrobinso]

Hi, Yes I do plan to support all IGV hosted genomes, however not via the .genome file. The plan is support a json representation that is common to IGV and igv.js. That is not developed yet in IGV.

In the meantime you can use the "reference" object to specify paths to fasta, index, and cytoband ideogram (optional). I don't recognize hg20, I think you mean hg38. You can use the following paths for that assembly

https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai

cytoband https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt

for an annotation track you can use

https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/genes/gencode.v24.annotation.sorted.gtf.gz https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/genes/gencode.v24.annotation.sorted.gtf.gz.tbi (index)

On Fri, May 5, 2017 at 9:12 AM, Viliam Rockai notifications@github.com wrote:

While the hg18 and hg19 references are supported by default, is there any plan to support more references? I'm interested in grch38/hg20 in particular.

The desktop IGV browser can accept a .genome file, like: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome

Is this file type somehow supported in IGV.js, too? What are my options if I want to use hg20 with IGV.js?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/363, or mute the thread https://github.com/notifications/unsubscribe-auth/AA49HIpkMKZ8zKs-2bBKeaqSHK_n09nVks5r20p8gaJpZM4NSHy7 .

[vrockai]

Thanks a lot! Sorry about the confusion. As you have correctly assumed, I had hg38 in mind. However, the https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt file doesn't seem to render the cytoband correctly:

By any chance, do you host an annotation track for hg18 somewhere, too? Or this SNP file used in examples for hg18 and hg38: https://github.com/igvteam/igv.js/blob/master/examples/beta.html#L83

Is there a list of hosted files by igv.broadinstitute.org somewhere?

[jrobinso]

There is not a list per se, but its easily discoverable. First step is the "data server registry" file for the genome, a flat list of xml files. For genomes of interest

http://data.broadinstitute.org/igvdata/hg18_dataServerRegistry.txt http://data.broadinstitute.org/igvdata/hg19_dataServerRegistry.txt http://data.broadinstitute.org/igvdata/hg38_dataServerRegistry.txt

Then look through the XMLs listed. For your purposes the "annotation" xml is probably the most interesting, for example

http://www.broadinstitute.org/igvdata/annotations/hg18/hg18_annotations.xml

Its might also be helpful to run IGV desktop, select a genome, then select "File > Load from server" to see what is there.

[jrobinso]

Modifying this to "add more references"

[jrobinso]

The list is longer now, and growing, current list is at https://s3.amazonaws.com/igv.org.genomes/genomes.json. The cytoband rendering bug for some assemblies is noted in another issue.

[adebali]

How about bacterial genomes, like E coli? If not, how can I build custom reference genomes? Is there any documentation on this? @jrobinso

[jrobinso]

https://github.com/igvteam/igv.js/wiki/Reference-Genome-2.0