abemus (version 1.0.2)

split_pacbam_bychrom: Split PaCBAM ouputs by chromosomes

Description

Split PaCBAM ouputs by chromosomes

Usage

split_pacbam_bychrom(targetbed, pacbamfolder, pacbamfolder_bychrom)

Arguments

targetbed

Genomic regions in the BED tab-delimited format.

pacbamfolder

Folder with original outputs generated by PaCBAM. This folder should contain both .pabs and .pileups files.

pacbamfolder_bychrom

Output folder in which subfolders for each sample will be created.

Value

Original data from PaCBAM split by chromosome in separate files, these are saved in two sub-folders 'pileup' and 'snvs', organized by sample.

Examples

# NOT RUN {
targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
pacbamfolder <- system.file("extdata", "pacbam_data", package = "abemus")
pacbamfolder_bychrom <- tempdir()
split_pacbam_bychrom(targetbed,pacbamfolder,pacbamfolder_bychrom)
# }