Re: [Artemis-users] Problems viewing VCF files

[Tim Carver]

Hi Louis

You need to read in the bgzip'ed vcf file not the tabix index file. It is
expecting a file to be loaded with the suffix .vcf.gz rather than .tbi. It
will then automatically look for the index (.tbi) file in the same directory
as the VCF file.

Regards
Tim


On 3/17/12 2:48 PM, Louis Grandjean drlouisgrandj...@hotmail.com wrote:

 Dear All,
 
 I'm new to Artemis and have had problems reading in vcf files.  I've indexed
 the vcf files using bgzip and tabix as detailed in the manual and I'm also
 using the Artemis developer version 14.0.  First I load in the reference embl
 file with no problems then go to File  Read VCF and select my .tbi file
 output from tabix.  However nothing appears on the screen.  I'm not sure where
 I'm going wrong.  Any help would be gratefully appreciated.
 
 Best wishes 
 
 Louis
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[Artemis-users] Java web start with Artemis

[PIRA (Preethi Ramaiya)]

Hi

I would like to be able to serve up genomes with BAM files as shown in 
http://www.sanger.ac.uk/resources/software/artemis/ngs/. It is very handy for 
our end-users to be able to visualize the a NGS alignments in a familiar tool.

Is there a how to  set up artemis with Webstart  and bam files loaded per 
genome- how do you get from my genome file and the correspond .bam and .bai to 
the jlnp file that is needed by the web start.

- its probably obvious but I am new to web-start and would appreciate any help.

The server is running Ubuntu with Apache as the web server. It is set up with 
the right mime types for Java Webstart.


Thank you
Preethi



Best Regards
Preethi Ramaiya


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