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. |
— |
--minimum-coverage, -mc |
Minimum CpG coverage to consider. Can be a single integer or a list (e.g. 1,3,5). |
1 |
--t-step |
Step size for extrapolation factor (t) predictions. |
0.05 |
--t-max |
Maximum extrapolation factor (t). |
10.0 |
--compute_ci |
Compute confidence intervals using bootstrap replicates. |
False |
--bootstrap-replicates, -b |
Number of bootstrap replicates for CI computation. |
30 |
--conf |
Confidence level for bootstrap intervals. |
0.95 |
--mu |
Initial mu parameter for the negative binomial distribution in the EM algorithm. |
0.5 |
--size |
Initial size parameter for the negative binomial distribution in the EM algorithm. |
1.0 |
--mt |
Constraint for rational function approximations. |
20 |
--rrbs |
If set to True, MethylDackel will use the RRBS flag (--keepDupes). |
False |
--threads, -@ |
Number of threads to use. |
Available threads - 2 |
--keep-temporary-files, -k |
Keep temporary files after analysis. |
False |
--verbose |
Enable verbose logging. |
False |
--help, -h |
Print the help message and exit. |
— |
--version |
Print the package version. |
— |