| run.filtering.txt | R Documentation |
Run filtering on an ANNOVAR-annotated txt file
run.filtering.txt(variant.file, caller = c("consensus", "vardict",
"ides", "mutect"), output.directory = NULL, output.filename = NULL,
code.directory = NULL, log.directory = NULL, config.file = NULL,
job.dependencies = NULL, job.group = NULL, quiet = FALSE)
variant.file |
Path to variant file |
caller |
String giving variant caller that was used (affects which filters were applied. |
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 |
quiet |
Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging. |