Proper regex to mark duplicates using Picard tools on SOLiD data

anishanish Member
edited December 2014 in Ask the GATK team


I'm having trouble removing duplicates using Picard tools on SOLiD data. I get a regex not matching error.

The reads have the following names:





And I don't think Picard tools is able to pick these read names with its default regex.

I tried to change the default regex. This time it does not throw an error, but it takes too long and times out (out of memory). I suspect I'm not giving the right regex. Here is my command:

java -jar $PICARD_TOOLS_HOME/MarkDuplicates.jar I=$FILE O=$BAMs/MarkDuplicates/$SAMPLE.MD.bam M=$BAMs/MarkDuplicates/$SAMPLE.metrics READ_NAME_REGEX="([0-9]+)([0-9]+)([0-9]+).*"

Any help is appreciated. Thanks!


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