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