Re: [galaxy-user] problem using Depth of Coverage (GATK)

[Jennifer Jackson]

Hello Gema,

The tool group GATK-Tools (beta) is not indexed to function with the 
hg19 genome.


As an alternative on the public Main Galaxy server, please see the tool 
group  BEDTools. There are two tools here that calculate coverage 
using BAM data as input.


Another alternative is to set up either a local or cloud Galaxy, obtain 
the hg19 indexes from GATK, then run the analysis there. If you wish to 
try this please see:

http://getgalaxy.org
http://usegalaxy.org/cloud

Take care,

Jen
Galaxy team

On 4/7/13 11:41 PM, Gema Sanz wrote:


Hello, I´m trying to use depth of coverage to check the coverage of my 
reads. I already have the bam files (created with sam to bam) but they 
are still not recognized by depth of coverage and I got this error 
message:


Sequences are not currently available for the specified build

I used human (homo sapiens) hg19 full for mapping but I can´t select 
it, it only allows b37 version. I tried to change the build in edit 
parameters to b37 and then it is recognized but I got another error at 
the end of the analysis.


Any suggestions?

Thank you very much in advance

Gema



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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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[galaxy-user] problem using Depth of Coverage (GATK)

[Gema Sanz]

Hello, I´m trying to use depth of coverage to check the coverage of my
reads. I already have the bam files (created with sam to bam) but they are
still not recognized by depth of coverage and I got this error message:

Sequences are not currently available for the specified build

I used human (homo sapiens) hg19 full for mapping but I can´t select it,
it only allows b37 version. I tried to change the build in edit parameters
to b37 and then it is recognized but I got another error at the end of the
analysis.

Any suggestions?

Thank you very much in advance

Gema

 

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/