Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Proper regex to mark duplicates using Picard tools on SOLiD data
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!