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