Difference between revisions of "ExomeCNV"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 21:20, 6 December 2019

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_EXOMECNV_DIR - installation directory





Validation

  • Validated 4/5/2018