Feature tracks: details do not pop up for insertions

[Christoph Schmidt]

Hi everyone,

I would like to build a track, where I can click on features to open the attached links in a browser.

When zooming into feature tracks (e.g. dbSNP 1.3.7 loaded from Server) the detail box is not displayed anymore, when hover over or clicking on an insertion. The insertion is shown only as a small line between two bases and is not clickable. When zooming out at some point the same insertion suddenly is clickable.(e.g. rs147093981 chr1:10383-10383 )

Not only the additional information does not show up, it is also not possible to open an external link for those (e.g. for defined URLs in custom bed-files with track line).

Is there any way to show insertions that are clickable when zooming in? (The detail box shows up for the same insertions loaded as a vcf-file, but for vcf-files there is no option for external links.)

Thanks,

chris

[Christoph Schmidt]

I forgot to mention: I tried IGV 2.3.81 and 2.3.90

[James Robinson]

Hi,  I'll look into it.    The problem stems from how that feature is encoded in the dbSNP bed file.   Note its position in bed coordinates has a width of zero.   The convention on insertion positions in VCF files is different and that's why it works there.

So I'll make a fix to handle "0" length features.    If you have a vcf file with rs147093981 it would be helpful to know what position is encoded for that,  but if not I can look it up.

On Fri, Feb 3, 2017 at 5:04 AM, Christoph Schmidt <schmidt.ch...@gmail.com> wrote:

I forgot to mention: I tried IGV 2.3.81 and 2.3.90

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[Christoph Schmidt]

From the dbSNP ftp (ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b149_GRCh37p13/VCF/All_20161121.vcf.gz)

...
1       10383   rs147093981     A       AC      .       .       RS=147093981;RSPOS=10383;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP
...

Thanks for the help!

[Jim Robinson]

Hi, this should be fixed (release 2.3.91).  Also,  I updated the hg19 snp track to 147.

[Christoph Schmidt]

Hi, thanks for the quick fix! Looks nice! :)

2017-02-07 22:14 GMT+01:00 Jim Robinson <jrob...@broadinstitute.org>:

Hi, this should be fixed (release 2.3.91).  Also,  I updated the hg19 snp track to 147.

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