Any way to get COSMIC track working? (under Load from Server...Annotations ... Disease ...)

277 views
Skip to first unread message

Paul Kowalski

unread,
Feb 1, 2015, 8:30:51 PM2/1/15
to igv-...@googlegroups.com
Hi -
IGV is an amazing piece of work, but as I use it to look at tumor vs normal leukemia samples, it would be great if the COSMIC track (known cancer associated mutations) would work. Currently it fails as below. 
Apparently COSMIC (at the Sanger) still hosts the DAS server at http://das.sanger.ac.uk/das/cosmic_mutations_GRCh37 so maybe it's a simple fix? 
cheers in advance
Paul



INFO [2015-02-01 20:26:13,522]  [TrackLoader.java:112] [pool-2-thread-1]  Loadin
INFO [2015-02-01 20:26:14,508]  [MessageUtils.java:60] [pool-2-thread-1]  <html>
br>Check file extension

Jim Robinson

unread,
Feb 1, 2015, 9:35:30 PM2/1/15
to igv-...@googlegroups.com
Hi Paul,

The first bit was easy to fix,  but after getting past that I am getting errors from the cosmic das server.  For example, their test query returns an error:  http://das.sanger.ac.uk/das/cosmic_mutations_GRCh37/features?segment=7:139887581,150077687.    I'll file an error report there.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/5cc1ecde-2386-44b0-9ad2-a1d38d3429f3%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Jim Robinson

unread,
Feb 4, 2015, 12:30:29 PM2/4/15
to igv-...@googlegroups.com
Hi,

Unfortunately I received this response from Sanger.  I will remove the Cosmic link from the menu until we can figure out another way to support this resource.

Dear Jim,

Thanks for contacting the COSMIC help desk.

I'm afraid DAS is no longer supported and we have shutdown our DAS sources.

Kind regards,

Dave Beare

Jim Robinson

unread,
Feb 5, 2015, 2:10:34 PM2/5/15
to igv-...@googlegroups.com
Hi,  apparently Sanger is no longer supporting the DAS server.  Further, they now have a restrictive license on the COSMIC database that makes it impossible for us to offer it from IGV.  This is unfortunate.  As a workaround I suggest you download the Mutation database, then rearrange columns to create, for example, a bed or gff track and load to igv.   In the meantime I will work on direct support for the downloaded file  (the "Mutation" export),  but you will have to download it and load from the file menu.

Jim

Paul Kowalski

unread,
Feb 5, 2015, 3:22:17 PM2/5/15
to igv-...@googlegroups.com
Thanks for figuring it out! Too bad about Sanger's license and DAS removal. Will give a shot at making a .gff track...
cheers
Paul

Jon Andreas Lorentzen

unread,
May 14, 2015, 3:19:52 AM5/14/15
to igv-...@googlegroups.com
Hi. Any solutuion for a direct support of the cosmic mutation export file? I am not familiar with how to make "a bed of gff track". 

Jim Robinson

unread,
May 14, 2015, 9:58:22 AM5/14/15
to igv-...@googlegroups.com
Hi,

I don't have a solution for the export file yet, however they do provide "vcf" file downloads for coding and non-coding mutations (see http://cancer.sanger.ac.uk/cosmic/download, bottom of page).  For example, the path for hg38 is sftp://sftp-cancer.sanger.ac.uk/files/grch38/cosmic/v72/VCF/CosmicCodingMuts.vcf.gz.    After downloading this file gunzip it, then load it directly into igv.   It will give you a warning about size and suggestion to index the file, click "Go" to create the index.

The display is not ideal,  but it does work.  

We would like to provide direct support for Cosmic as we used to do, but Sanger's new licensing terms forbid it.   If you have questions or would like provide feedback on this please contact  cosmic-tr...@sanger.ac.uk.

Jim

Jon Andreas Lorentzen

unread,
May 21, 2015, 2:55:01 AM5/21/15
to igv-...@googlegroups.com
Thanks, it is working. However, my data will not align properly with hg38. Hg19 works fine. 

Jon

Jim Robinson

unread,
May 21, 2015, 2:23:57 PM5/21/15
to igv-...@googlegroups.com
I'm not sure I understand the comment, but VCF files will be aligned to a specific assembly, so you have to download the file for the assembly of interest (if they have it).

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
Reply all
Reply to author
Forward
0 new messages