Commit 31b79a96 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

algo.org: help on germline selection

parent cf74fa88
......@@ -117,6 +117,25 @@ By default, the two output files are named =out/basename.vidjil= in =out/basenam
Launching vidjil with =-h= option provides the list of parameters that can be
used. We detail here the options of the main =-c clones= command.
** Germline selection
#+BEGIN_EXAMPLE
Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c germlines)
-V <file> V germline multi-fasta file
-D <file> D germline multi-fasta file (and resets -m, -M and -w options), will segment into V(D)J components
-J <file> J germline multi-fasta file
-G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)
-g <path> multiple germlines (in the path <path>, takes TRA, TRB, TRG, TRD, IGH and IGL and sets window prediction parameters)
#+END_EXAMPLE
There are three different ways
- Options such as =-G germline/IGH= or =-G germline/TRG= select one germline system.
- The =-V/(-D)/-J= options enable to select individual V, (D) and J repertoires (fasta files).
This allows in particular to select incomplete rearrangement using V or J repertoires.
- The =-g germline/= option launches the analysis on the six germlines (TRG and IGH are tested first, then the other ones).
Now the seed and window parameters are hard-coded for each germline. In a future release, the mechanism will be more flexible
and will parse the =germline/germlines.data= file.
** Main algorithm parameters
#+BEGIN_EXAMPLE
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