I'm not sure I really understand your question but if the metrics described at http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics are of use, you could try the picard hybrid selection metrics Galaxy tool or use it on the command line. Otherwise perhaps you can get a more helpful response if you provide a clear explanation of the data formats you have and the measures you want.

On Wed, Dec 21, 2011 at 2:59 AM, Antoine ROUSSELIN <a.rousselin@baclesse.fr> wrote:

hello,
I'm looking for a tool (or command line) to determine the % On-Off target + or - 50 bp of exon from my capture file but not annotated (!!!). Capture SureSelect agilent home.

Current pipeline:
GAIIx Illumina
CASAVA1.8
IGV
CNV-seq
SAMtools
BEDtools
GALAXY
NextGENe

Please HELP

ROUSSELIN Antoine
Clinical Biology and Oncology Laboratory
Centre François BACLESSE
France/Caen
a.rousselin@baclesse.fr
Tel : (33) 02.31.45.40.44
Fax : (33) 02.31.45.50.53

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