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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