Convert highlights to histogram about genoverse

[simonbrent]

I don't really understand what you're trying to do.

[alisha2468]

Hi simon, When you drag and drop a vcf file into the genome browser, a new track is generated showing the SNVs at each position. I want to generate histograms of SNP density at each position instead Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: Simon Brent <[email protected]> Sent: Thursday, March 15, 2018 10:03:58 AM To: wtsi-web/Genoverse Cc: Ahamed, Alisha; Author Subject: Re: [wtsi-web/Genoverse] Convert highlights to histogram (#49) I don't really understand what you're trying to do. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#49 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AjpKbw9wltcP8XT15Y1rNf_j5mz4EbQLks5tejyOgaJpZM4SqjWf>.

[simonbrent]

I'm afraid that isn't really possible at this time. I would recommend creating a back-end process that reads the VCF and outputs data as required by Genoverse.Track.Graph.Bar, but that won't really help with the drag and drop use case.

[alisha2468]

Thank you Simon! If possible, could you give me an example please? Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: Simon Brent <[email protected]> Sent: Friday, March 16, 2018 11:38:47 AM To: wtsi-web/Genoverse Cc: Ahamed, Alisha; Author Subject: Re: [wtsi-web/Genoverse] Convert highlights to histogram (#49) I'm afraid that isn't really possible at this time. I would recommend creating a back-end process that reads the VCF and outputs data as required by Genoverse.Track.Graph.Bar, but that won't really help with the drad and drop use case. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#49 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AjpKb6nLt-VRF2mmXzASuW41CuJnQUy2ks5te6RHgaJpZM4SqjWf>.

[simonbrent]

Not really...you'll need a VCF parser (like bcftools), a web server written in the language of your choice which
a) can accept VCF uploads/extract data from URLs where VCFs are stored
b) has an endpoint that extracts data from a VCF for a region it and returns a JSON array where each entry is in the form { chr: 1, start: 100, end: 100, height: 5 } // height = the number of variants found at that location

[alisha2468]

Hi Simon,
I tried parsing the VCF but it does not work when extended from Graph.Bar or Graph.Line but works otherwise. Any idea why that is happening?

[alisha2468]

Hi Simon, its working now and i am able to view the histograms as well. Any tips on smoothening the histograms? i am currently trying d3.js. Any inputs would be appreciated!