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?

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