This is typically used to either remove host DNA, or keep reads mapping to a known reference. If the BAM-file has paired reads then BOTH reads need to be mapped (flag 0x2); otherwise (flag 0x4)
Usage
BascetFilterAlignment(
bascetRoot,
numLocalThreads = NULL,
inputName,
outputName,
keepMapped = FALSE,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- numLocalThreads
Number of threads to use. Default is the maximum, taken from runner settings
- inputName
Name of input shards (BAM-file format)
- outputName
Name of output shards (BAM-file format)
- keepMapped
Keep the mapped reads (TRUE) or unmapped (FALSE)
- overwrite
Force overwriting of existing files. The default is to do nothing files exist
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance