ExomeCNV

From UFRC
Revision as of 19:35, 5 April 2018 by Jakers (talk | contribs)
Jump to navigation Jump to search

Description

exomecnv website  

ExomeCNV is an R package tailored to detection of CNV (Copy-Number Variants) and LOH (Loss of Heterozygosity) from exome sequencing data. It exploits the unique discrete feature of exon definitions and incredible cross-sample consistency of depth-of-coverage. ExomeCNV is most suitable when paired samples (e.g. tumor-normal pair) are available. Both of the paired samples should be processed and sequenced in a similar manner (e.g. same library prep, sequencer, average depth-of-coverage, etc.). The inputs necessary for ExomeCNV are

  1. bam/pileup file
  2. exome definition file (.bed)
  3. a conservative approximation of sample admixture rate.


Required Modules

Serial

  • exomecnv

System Variables

  • HPC_{{#uppercase:exomecnv}}_DIR - installation directory





Validation

  • Validated 4/5/2018