I fixed it, Thanks.
It was because I aligned to different genomes in BWA and GATK steps

2012/4/3 Lilach Friedman <lilac...@gmail.com>

> Hi Galaxy Team,
> I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined
> results as input.
> My steps were:
> 1. BWA alignment
> 2. SAM-to-BAM
> 3. rmdup.
> when I'm trying to give 3 (rmdup results) as an input to GATK
> DepthOfCoverage, an error appears: "
>   Sequences are not currently available for the specified build."
> What did I do wrong?
> Many thanks!
>    Lilach
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