Rxivist logo

Parliament2: Fast Structural Variant Calling Using Optimized Combinations of Callers

By Samantha Zarate, Andrew Carroll, Olga Krashenina, Fritz J Sedlazeck, Goo Jun, William Salerno, Eric Boerwinkle, Richard Gibbs

Posted 23 Sep 2018
bioRxiv DOI: 10.1101/424267

Here we present Parliament2: a structural variant caller which combines multiple best-in-class structural variant callers to create a highly accurate callset. This captures more events than the individual callers achieve independently. Parliament2 uses a call-overlap-genotype approach that is highly extensible to new methods and presents users the choice to run some or all of Breakdancer, Breakseq, CNVnator, Delly, Lumpy, and Manta to run. Parliament2 applies an additional parallelization framework to speed certain callers and executes these in parallel, taking advantage of the different resource requirements to complete structural variant calling much faster than running the programs individually. Parliament2 is available as a Docker container, which pre-installs all required dependencies. This allows users to run any caller with easy installation and execution. This Docker container can easily be deployed in cloud or local environments and is available as an app on DNAnexus.

Download data

  • Downloaded 2,839 times
  • Download rankings, all-time:
    • Site-wide: 2,027 out of 89,387
    • In bioinformatics: 360 out of 8,433
  • Year to date:
    • Site-wide: 4,208 out of 89,387
  • Since beginning of last month:
    • Site-wide: 10,233 out of 89,387

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News