vcf not loading vcf

Peio Ziarsolo

unread,

Mar 21, 2012, 4:35:31 AM3/21/12

to igv-...@googlegroups.com

Hello,
I am trying to load a vcf file into IGV and I am having some problems. I
have prepared a sample vcf with just one snv and it stills does not
loads despite passing the vcf-validator tool.

I have indexed the file with tabix and igv-tools and IGV return the same
output error log in both cases:

------------------------------
An error occurred accessing : /path/to/file.vcf
null
------------------------------

INFO [2012-03-21 09:23:17,702] [TrackManager.java:246]
[pool-2-thread-4] Loading1 resources.
ERROR [2012-03-21 09:23:17,709] [TrackLoader.java:273]
[pool-2-thread-4] java.lang.NullPointerException
ERROR [2012-03-21 09:23:17,709] [TrackManager.java:285]
[pool-2-thread-4] Error loading tracks
org.broad.igv.exceptions.DataLoadException: <html>An error occurred
while accessing: /home/jope/work_in/igv_bug/snvs_to_igv.vcf<br>null
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:274)
at org.broad.igv.track.TrackManager.load(TrackManager.java:322)
at org.broad.igv.track.TrackManager$1.run(TrackManager.java:267)
at
org.broad.igv.track.TrackManager.loadResources(TrackManager.java:294)
at org.broad.igv.ui.IGV$5.run(IGV.java:688)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:74)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)

-------------------

I am attaching the genome(just one seq) and the vcf file. Is this a bug
or am I doing something wrong?

Thanks in advance
Peio Ziarsolo

Peio Ziarsolo

unread,

Mar 21, 2012, 4:50:57 AM3/21/12

to igv-...@googlegroups.com

I forgot the files..
Sorry

Peio Ziarsolo
az., 2012.eko marren 21a 09:35(e)an, Peio Ziarsolo(e)k idatzi zuen:

contigs.fasta

snvs_to_igv.vcf

Craig Berry

unread,

Mar 21, 2012, 6:05:10 AM3/21/12

to igv-...@googlegroups.com

Which version of IGV are you using?

I believe there was a bug with parsing vcf files that only contained a single variant, so you might want to try with the early access release.

HTH

Craig

Peio Ziarsolo

unread,

Mar 21, 2012, 6:36:54 AM3/21/12

to igv-...@googlegroups.com

az., 2012.eko marren 21a 11:05(e)an, Craig Berry(e)k idatzi zuen:

> Which version of IGV are you using?

I am using version 2.0.34.

>
> I believe there was a bug with parsing vcf files that only contained a
> single variant, so you might want to try with the early access release.

I have tried with a vcf with two snvs and it works.

I have seen that my previous error(not the error with the sample file)
was because I was indexing wrong the vcf file. I have solved all my issues.

Thanks!
Peio

>
> HTH
>
> Craig
>
> On 21 March 2012 08:50, Peio Ziarsolo <pzia...@upv.es

Reply all

Reply to author

Forward