CLI
To access the help menu:
$ pydamage --help
The list of arguments of options is detailed below
pydamage
PyDamage: Damage parameter estimation for ancient DNA
Author: Maxime Borry
Contact: <borry[at]shh.mpg.de>
Homepage & Documentation: github.com/maxibor/pydamage
pydamage [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
- -o, --outdir <outdir>
Output directory
- Default
pydamage_results
analyze
Run the PyDamage analysis
BAM: path to BAM/SAM/CRAM alignment file. MD tags need to be set.
pydamage analyze [OPTIONS] BAM
Options
- -w, --wlen <wlen>
Window length (in bp) for damage modeling
- Default
20
- -p, --process <process>
Number of processes for parallel computing
- Default
2
- -s, --show_al
Display alignments representations
- -pl, --plot
Write damage fitting plots to disk
- -vv, --verbose
Verbose mode
- -f, --force
Force overwriting of results directory
- -g, --group
Use entire BAM file as single reference for analyis (ignore reference headers)
Arguments
- BAM
Required argument
cite
Get pydamage citation in bibtex format
pydamage cite [OPTIONS]
filter
Filter PyDamage results on predicted accuracy and qvalue thresholds.
CSV: path to PyDamage result file
pydamage filter [OPTIONS] CSV
Options
- -t, --threshold <threshold>
Predicted accuracy filtering threshold. Set to 0 for finding threshold with kneed method
- Default
0.5
Arguments
- CSV
Required argument