and another question:
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

2012/4/2 Lilach Friedman <lilac...@gmail.com>

> Hi,
>
> I have NGS results of DNA enriched for exons with an AllExon kit (Agilent).
> I have a bed file with the list of targeted sequences.
> I want to use GATK DepthOfCoverage to compare the results to the bed file
> and to get all the targets that were covered by <n reads.
>
> How can I do that with Galaxy on the web? or in Amazon?
>
> My question has 2 parts:
> 1. How can I specify the target intervals in Galaxy on the web?  (the "-L"
> command in Unix commandline)
> 2. How can I ask the coverage for single bases instead of statistics?
>
>
> Thanks,
>    Lilach
>
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