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 FASTA: path to reference FASTA file

pydamage [OPTIONS] BAM FASTA

Options

--version

Show the version and exit.

-w, --wlen <wlen>

Window length for damage modeling

Default

35

-p, --process <process>

Number of processes

Default

2

-m, --mini <mini>

Minimum reads aligned to consider reference

Default

1000

-c, --cov <cov>

Minimum coverage to consider reference

Default

8

-s, --show_al

Show alignments representations

-pl, --plot

Make the damage plots

--verbose

Verbose mode

-o, --outdir <outdir>

Output directory

Default

pydamage_results

--force

Force overwriting of results directory

Arguments

BAM

Required argument

FASTA

Required argument