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 <lilachfr@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