Displaying variants on GBrowse and/or JBrowse

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Displaying variants on GBrowse and/or JBrowse

Lau, Branden M - (bmlau)
Hello,

I'm trying to figure out how to use genome browsers to display either vcf data or gff3 data. I've tried uploading a gff file containing arabidopsis data onto TAIR's genome browser (http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/)http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ and no matter where I look on the genome, I see no variants displayed. I want to know if someone can explain to me how to display variants onto GBrowse (or JBrowse for that matter) and whether or not I'm missing something obvious that someone can explain to me? 

I've attached the files I've been trying to use, one is a vcf file and the other is a gff3 formatted version of the vcf file. 

Thanks,
Branden

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iplant_vcf_to_gff.gff (32K) Download Attachment
Outputfile (18K) Download Attachment
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Re: Displaying variants on GBrowse and/or JBrowse

Alexey Morozov
Well, in gbrowse the only features shown are ones that have a specific track, so you'll have to make one for variants. In your case they are of type 'sequence_feature' (I guess). So you need a track definition like following (it should be in your *.conf file for gbrowse):

default_tracks=Seq_features

[Seq_features]
database=<insert your db here>
feature=sequence_feature
key=Variants
balloon click=sub{ <Insert some perl magic that shows data from last column of GFF>}

Of course, you also need to define a database, point gbrowse to this conf file via GBrowse.conf and so on, see http://gmod.org/wiki/GBrowse_2.0_Configuration_HOWTO

2014-10-03 4:55 GMT+09:00 Lau, Branden M - (bmlau) <[hidden email]>:
Hello,

I'm trying to figure out how to use genome browsers to display either vcf data or gff3 data. I've tried uploading a gff file containing arabidopsis data onto TAIR's genome browser (http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/)http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ and no matter where I look on the genome, I see no variants displayed. I want to know if someone can explain to me how to display variants onto GBrowse (or JBrowse for that matter) and whether or not I'm missing something obvious that someone can explain to me? 

I've attached the files I've been trying to use, one is a vcf file and the other is a gff3 formatted version of the vcf file. 

Thanks,
Branden

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--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

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