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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The Galaxy User list should be used for the discussion of
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