run_bcftools | R Documentation |
Run bcftools
run_bcftools(
command = NULL,
input = NULL,
output = NULL,
regions = NULL,
parallel = FALSE,
cores = 4,
execute = TRUE,
bcftools = NULL,
version = NULL
)
command |
bcftools command to run, at present can only choose isec, view or sort |
input |
vcf files |
output |
ouput directory or file |
regions |
Bed formatted regions of interest file |
parallel |
Run in parallel, default set to FALSE |
cores |
Number of cores/threads to use for parallel processing, default set to 4 |
execute |
Whether to execute the commands or not, default set to TRUE |
bcftools |
Path to the bcftools program, required |
version |
Returns the version number |
A list with the bcftools commands
## Not run:
bcftools.path <- "/software/bcftools-v1.9/bin/bcftools"
bcftools.version <- run_bcftools(bcftool = bcftools.path,
version = TRUE)
bcftools.version[1]
# bcftools intersect
command <- "isec"
vcfs <- c("test1.vcf","test2.vcf")
vcfs <- paste(vcfs, collapse = " ")
out.directory <- "test_directory"
bcftools.cmd <- run_bcftools(command = command,
input = vcfs,
output = out.directory,
execute = FALSE,
bcftools = bcftools.path)
bcftools.cmd
## End(Not run)
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