deepToolss 3.3.0用户手册
Get help
bamCoverage --help
Parameters of decrease the run time
numberofProcessors
多进程 e.g. --numberofProcessors 10
region
仅对基因组某个位置处理 e.g. --region chr2 or --region chr2:100000-200000
Filtering BAMs while processing
ignoreDuplicates
Reads with the same orientation and start position will be considered only once. If reads are paired, the mate is also evaluated
minMappingQuality
Only reads with a mapping quality score of at least this are considered
samFlagInclude
Include reads based on the SAM flag.
samFlagExclude
Exclude reads based on the SAM flags