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hapcompass website  

HapCompass implements a novel HAPCOMPASS algorithm for haplotype assembly of densely sequenced human genome data. The algorithm operates on a graph where SNPs are nodes and edges are defined by the sequencing reads and viewed as supporting evidence of co-occuring SNP alleles in a haplotype.

Environment Modules

Run module spider hapcompass to find out what environment modules are available for this application.

System Variables

  • HPC_HAPCOMPASS_DIR - installation directory
  • HPC_HAPCOMPASS_DOC - documentation directory
  • HPC_HAPCOMPASS_EXE - examples directory

Additional Information

To set the heap memory to be used by a java program export the _JAVA_OPTIONS variable in the environment the program runs in - either on the command line, in a personal module, or in a job script. For example,

export _JAVA_OPTIONS="-Xms1g -Xmx4g"

will set Java heap memory usage to a minimum of 1g and a maximum of 4g. Please note that _JAVA_OPTIONS environment variable overrides the respective command-line arguments. For example, the above '_JAVA_OPTIONS' variable will override the '-Xmx500m' argument in

java -Xmx500m -jar someprogram.jar....