Lumpy v0.2.12

Lumpy is a probabilistic framework to integrate multiple structural variation signals such as discordant paired-end alignments and split-read alignments.

Accessing the software

To load the module:

$ module load apps/lumpy/v0.2.12

An example command to include in your job script:

lumpy \
-mw 4 \
-tt 0 \
-pe id:sample,read_group:rg1,bam_file:sample.discordants.bam,histo_file:sample.lib1.histo,mean:500,stdev:50,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,min_mapping_threshold:20 \
-pe id:sample,read_group:rg2,bam_file:sample.discordants.bam,histo_file:sample.lib2.histo,mean:500,stdev:50,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,min_mapping_threshold:20 \
-sr id:sample,bam_file:sample.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20 \
> sample.vcf

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the Lumpy website for more information regarding this application.

Last modified: 1 December 2017


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