[Gmod-gbrowse] 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

[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

Post by 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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