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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