Description Usage Arguments Value
View source: R/run.annovar.vcf.R
Run ANNOVAR on a VCF file
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vcf.file |
Path to VCF file |
output.directory |
Path to output directory |
output.filename |
Name of resulting VCF file (defaults to SAMPLE_ID.vcf) |
code.directory |
Path to directory where code should be stored |
log.directory |
Path to directory where log files should be stored |
config.file |
Path to config file |
job.dependencies |
Vector with names of job dependencies |
job.group |
Group job should belong to |
job.name |
Name of job to be submitted |
isis |
Logical indicating whether VCF files are from the isis (MiniSeq) variant caller |
quiet |
Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging. |
verify.options |
Logical indicating whether to run verify.varitas.options |
None
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