MAINTENANCE OUTAGE: The University Wiki Service will undergo maintenance on September 26th, 2017, from 6 pm to 8 pm. During this 2 hour time period https://wikis.utexas.edu may be unavailable. Users are advised to save content locally that may be needed during this time and to otherwise save all edits as unsaved work may be lost. Please contact the UT Service Desk at 512-475-9400 for any questions.
The University Wiki Service has upgraded the Confluence Server software, from version 5.9.14 to 5.10.8. Please refer to the knowledge base article, KB0015891, for a high level summary of upgrade changes. Thank you!
Skip to end of metadata
Go to start of metadata
 Learn more about Picard's Mark Duplicates

If you want to run Picard's Mark Duplicates on Lonestar, do roughly this:

module load picard
# "picard" is not the name of the tool; picard is a collection of java .jar files that do things, so we have to figure out where they are and which ones they are, like this:
ls $TACC_PICARD_DIR
# Now to run Mark Duplicates, do something like:
java -Xmx2g -jar $TACC_PICARD_DIR/MarkDuplicates.jar INPUT=all.bowtie.sorted.bam OUTPUT=all.bowtie.sorted.dedup.bam METRICS_FILE=all.bowtie.sorted.dedup.bam.metrics ASSUME_SORTED=TRUE

The output metrics file is required and worth screening before you go further.

 Learn more about picard on Fourierseq

Picard is also installed on fourierseq at /usr/local/genome/bin and the jar files are in fourierseq user's paths.

General syntax for using picard jar files:

java -Xmx4g -jar /usr/local/genome/bin/jarfilename

 

 

Find picard document here

  • No labels