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