To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

GenomeSTRIP slow

Hi all,
Recently, I am trying to identify CNV(100k ~ 10MB) from PE data with GenomeSTRIP.
I followed the instruction
with the command like
java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R path_to_rmd_dir/reference_genome.fasta \
-I input_bam_files.list \
-md output_metadata_directory \

  I only input 1 bam file. The preprocess took several hours and output some empty folders.
  I am not sure if it had been run properly, and why it is so slow.


Sign In or Register to comment.