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

BAM: path to BAM/SAM/CRAM alignment file. MD tags need to be set.

pydamage [OPTIONS] BAM

Options

--version

Show the version and exit.

-w, --wlen <wlen>

Window length (in bp) for damage modeling

Default

35

-p, --process <process>

Number of processes for parallel computing

Default

2

-o, --outdir <outdir>

Output directory

Default

pydamage_results

-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