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Discovar

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DISCOVAR is a variant caller and small genome assembler that currently takes, as input, Illumina reads of length 250 or longer — produced on MiSeq or HiSeq 2500 — and from a single PCR-free library. DISCOVAR can call variants on a region by region basis, potentially tiling an entire large genome. DISCOVAR variant calling is under active development and transitioning to VCF.

This work has been funded by the National Human Genome Research Institute and National Institute of Allergy and Infectious Diseases.

On Helix

Currently, there are two versions available on the systems. To call a variant, on either system, type

 
 [user@helix ~]$ module load Discovar/[ver]
 [user@helix ~]$ Discovar READS=reads.bam OUT_HEAD=assembly REGIONS=1:50000-150000 REFERENCE=genome.fasta
  

or

 
 [user@helix ~]$ module load Discovardenova/[ver]
 [user@helix ~]$ Discovar READS=reads.bam OUT_HEAD=assembly REGIONS=1:50000-150000 REFERENCE=genome.fasta
  

To run either interactively on biowulf, at the porompt, type

sinteractive 

Documentation

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