BAM (positional) |
Path to a single .bam file or multiple files (e.g. files/*.bam). |
— |
--outdir, -o |
Output directory. |
./output |
--fasta |
Path to the reference genome FASTA file. If not provided, it will be automatically downloaded based on --genome. |
— |
--genome |
Genome used for alignment. Options: hg19, hg38, GRCh37, GRCh38, mm10, mm39. |
— |
--downsampling-percentages, -ds |
Comma-separated list of downsampling percentages (between 0 and 1, exclusive). |
0.1,0.2,0.4,0.6,0.8 |
--minimum-coverage, -mc |
Minimum CpG coverage to consider for saturation. Can be a single integer or a list (e.g. 1,3,5). |
3 |
--rrbs |
If set, MethylDackel will consider the RRBS nature of the data by adding the --keepDupes flag. |
False |
--threads, -@ |
Number of threads to use during downsampling. |
All available threads |
--keep-temporary-files |
Keep temporary files after analysis. |
False |
--verbose |
Enable verbose logging. |
False |
--help, -h |
Print the help message and exit. |
— |
--version |
Print the package version. |
— |