[Gmod-ajax] VCF track: show single VCF as multiple tracks, one per sample?

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[Gmod-ajax] VCF track: show single VCF as multiple tracks, one per sample?

Ben Bimber
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben

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Re: VCF track: show single VCF as multiple tracks, one per sample?

Sebastien Carrere
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :



Sebastien

Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


------------------------------------------------------------------------------
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Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape


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Re: VCF track: show single VCF as multiple tracks, one per sample?

Ben Bimber
Thanks for the reply.  I can see the use of this, but it's really nice to read off the VCF directly, so I might take a look at making some sort of plugin for it.  

If anyone has other similar examples I'd appreciate any pointers.

Thanks,
Ben

On Fri, Jul 8, 2016 at 11:58 AM, Sebastien Carrere <[hidden email]> wrote:
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :



Sebastien


Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


------------------------------------------------------------------------------
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present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
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[Gmod-ajax] VCF track: show single VCF as multiple tracks, one per sample?

Colin
I had done something like this directly from VCF at one point. I had sort of discontinued it but seeing as it could be useful I put it here https://github.com/cmdcolin/multivariantviewer


-Colin

On Fri, Jul 8, 2016 at 2:23 PM, Ben Bimber <[hidden email]> wrote:
Thanks for the reply.  I can see the use of this, but it's really nice to read off the VCF directly, so I might take a look at making some sort of plugin for it.  

If anyone has other similar examples I'd appreciate any pointers.

Thanks,
Ben

On Fri, Jul 8, 2016 at 11:58 AM, Sebastien Carrere <[hidden email]> wrote:
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :



Sebastien


Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


------------------------------------------------------------------------------
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present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: VCF track: show single VCF as multiple tracks, one per sample?

Keiran Raine
Hi Colin,

Thanks for sharing this it appears that this will solve some issue for us, 1 track instead of 50 in the config will help for some of our larger projects.

I can't tell from the link but is there the ability to filter the displayed data to a subset of samples in the interface?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 19 Jul 2016, at 20:05, Colin <[hidden email]> wrote:

I had done something like this directly from VCF at one point. I had sort of discontinued it but seeing as it could be useful I put it here https://github.com/cmdcolin/multivariantviewer


-Colin

On Fri, Jul 8, 2016 at 2:23 PM, Ben Bimber <[hidden email]> wrote:
Thanks for the reply.  I can see the use of this, but it's really nice to read off the VCF directly, so I might take a look at making some sort of plugin for it.  

If anyone has other similar examples I'd appreciate any pointers.

Thanks,
Ben

On Fri, Jul 8, 2016 at 11:58 AM, Sebastien Carrere <[hidden email]> wrote:
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :

<VcfBigWig.png>

Sebastien


Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
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present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape


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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: VCF track: show single VCF as multiple tracks, one per sample?

Ke Jiang
From the configuration example, looks like you can pick only a subset of the samples to show. I'll give it a try and report back.

Ke

On Wed, Jul 20, 2016 at 5:11 AM, Keiran Raine <[hidden email]> wrote:
Hi Colin,

Thanks for sharing this it appears that this will solve some issue for us, 1 track instead of 50 in the config will help for some of our larger projects.

I can't tell from the link but is there the ability to filter the displayed data to a subset of samples in the interface?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 19 Jul 2016, at 20:05, Colin <[hidden email]> wrote:

I had done something like this directly from VCF at one point. I had sort of discontinued it but seeing as it could be useful I put it here https://github.com/cmdcolin/multivariantviewer


-Colin

On Fri, Jul 8, 2016 at 2:23 PM, Ben Bimber <[hidden email]> wrote:
Thanks for the reply.  I can see the use of this, but it's really nice to read off the VCF directly, so I might take a look at making some sort of plugin for it.  

If anyone has other similar examples I'd appreciate any pointers.

Thanks,
Ben

On Fri, Jul 8, 2016 at 11:58 AM, Sebastien Carrere <[hidden email]> wrote:
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :

<VcfBigWig.png>


Sebastien


Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape


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present their vision of the future. This family event has something for
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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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Re: VCF track: show single VCF as multiple tracks, one per sample?

Ke Jiang
Looks like I'm having problems to show the track. Everything runs without errors, but the track doesn't show (see screenshot). There is no error in JS console, either. I'm attaching my configuration chunk, too. Am I missing anything? The VCF file has been configured as a regular variant track and it works fine.

Thanks!

Ke

[tracks . multivariantview ]
urlTemplate = ../../raw/Brnap/WGS_variants/SNP_all_final.filtered.pass.jbrowse.vcf.gz
storeClass = JBrowse/Store/SeqFeature/VCFTabix
type = MultiVariantViewer/View/Track/MultiVariantViewer
showLabels = true
showTooltips= true
style.height = 20
category = Variations


On Wed, Jul 20, 2016 at 8:36 AM, Ke Jiang <[hidden email]> wrote:
From the configuration example, looks like you can pick only a subset of the samples to show. I'll give it a try and report back.

Ke

On Wed, Jul 20, 2016 at 5:11 AM, Keiran Raine <[hidden email]> wrote:
Hi Colin,

Thanks for sharing this it appears that this will solve some issue for us, 1 track instead of 50 in the config will help for some of our larger projects.

I can't tell from the link but is there the ability to filter the displayed data to a subset of samples in the interface?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 19 Jul 2016, at 20:05, Colin <[hidden email]> wrote:

I had done something like this directly from VCF at one point. I had sort of discontinued it but seeing as it could be useful I put it here https://github.com/cmdcolin/multivariantviewer


-Colin

On Fri, Jul 8, 2016 at 2:23 PM, Ben Bimber <[hidden email]> wrote:
Thanks for the reply.  I can see the use of this, but it's really nice to read off the VCF directly, so I might take a look at making some sort of plugin for it.  

If anyone has other similar examples I'd appreciate any pointers.

Thanks,
Ben

On Fri, Jul 8, 2016 at 11:58 AM, Sebastien Carrere <[hidden email]> wrote:
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :

<VcfBigWig.png>


Sebastien


Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape


_______________________________________________
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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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multivariantview.png (93K) Download Attachment
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Re: VCF track: show single VCF as multiple tracks, one per sample?

Colin
Hi Ke, 
Not exactly sure but I think if you make style.height smaller it could fix it. For some reason larger style.height makes it blank. Can look into that

There also isn't filtering on rows yet but that could be a good feature!


-Colin

On Wed, Jul 20, 2016 at 10:21 AM, Ke Jiang <[hidden email]> wrote:
Looks like I'm having problems to show the track. Everything runs without errors, but the track doesn't show (see screenshot). There is no error in JS console, either. I'm attaching my configuration chunk, too. Am I missing anything? The VCF file has been configured as a regular variant track and it works fine.

Thanks!

Ke

[tracks . multivariantview ]
urlTemplate = ../../raw/Brnap/WGS_variants/SNP_all_final.filtered.pass.jbrowse.vcf.gz
storeClass = JBrowse/Store/SeqFeature/VCFTabix
type = MultiVariantViewer/View/Track/MultiVariantViewer
showLabels = true
showTooltips= true
style.height = 20
category = Variations


On Wed, Jul 20, 2016 at 8:36 AM, Ke Jiang <[hidden email]> wrote:
From the configuration example, looks like you can pick only a subset of the samples to show. I'll give it a try and report back.

Ke

On Wed, Jul 20, 2016 at 5:11 AM, Keiran Raine <[hidden email]> wrote:
Hi Colin,

Thanks for sharing this it appears that this will solve some issue for us, 1 track instead of 50 in the config will help for some of our larger projects.

I can't tell from the link but is there the ability to filter the displayed data to a subset of samples in the interface?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 19 Jul 2016, at 20:05, Colin <[hidden email]> wrote:

I had done something like this directly from VCF at one point. I had sort of discontinued it but seeing as it could be useful I put it here https://github.com/cmdcolin/multivariantviewer


-Colin

On Fri, Jul 8, 2016 at 2:23 PM, Ben Bimber <[hidden email]> wrote:
Thanks for the reply.  I can see the use of this, but it's really nice to read off the VCF directly, so I might take a look at making some sort of plugin for it.  

If anyone has other similar examples I'd appreciate any pointers.

Thanks,
Ben

On Fri, Jul 8, 2016 at 11:58 AM, Sebastien Carrere <[hidden email]> wrote:
Hi Ben,

To address this question we choose to convert our multisample VCF file into multiple BigWig files  (with values +1 for GT 0/0, -1 for 1/1 and 0 for ./.) - we do not have het samples in our file.
And we use the multibigwig plugin developped by Colin Diesh to display these files at once.
And it looks like this :

<VcfBigWig.png>


Sebastien


Le 08/07/2016 18:37, Ben Bimber a écrit :
Hello,

The ability of jbrowse to show a VCF file directly as a track is great.  I had one question: if this VCF file has multiple samples, is there any way to show it as multiple tracks, one per sample?  It could also work if I could create many tracks entries and somehow configure that each track to limit itself to one sample.  

The goal would be to make it easier for people to see where each sample has variation.  If doing this, I presume we only want non-homozygous reference positions to show.

Thanks for any help or ideas.

-Ben


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