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
- bam/pileup file
- exome definition file (.bed)
- a conservative approximation of sample admixture rate.
- HPC_EXOMECNV_DIR - installation directory
- Validated 4/5/2018