@@ -33,8 +33,8 @@ To choose where the annotations will be transfered, use these options:
Additionnal files that give informations about the transfer can be obtained with these options :
- ```-aln``` or ```--alignment``` : outputs the alignments of the annotated features in the source genome and in a target genome.
- ```-var``` or ```--variation``` : outputs the detail of the variations between the features in the source genome and in the target genome.
- ```-pav``` or ```--pav_matrix``` : outputs a presence-absence variation matrix to recapitulate the annotation transfers. Requires at least one option among ```-ann```, ```-aln``` and ```-var```.
<!-- could change the -pav requirements -->
- ```-pav``` or ```--pav_matrix``` : outputs a presence-absence variation matrix to recapitulate the annotation transfers. Requires the option ```-ann/--annotation```.
<!-- could change the -pav requirements to one among ann,var,aln, or no requirement-->
You can filter the annotations you transfer with these options :
- ```-cov``` or ```--coverage``` : specify the minimum requested coverage percentage between the original feature and the feature found in the target genome. Default is 80.
