Commit a4efbf7b authored by Mathieu Giraud's avatar Mathieu Giraud

doc/ update help, -i and -2

parent 780f3d7e
......@@ -209,14 +209,18 @@ Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all co
-g <path> multiple locus/germlines. In the path <path>, takes '' to select locus and parameters
Selecting '-g germline' processes TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations
A different '' file can also be provided with -g <file>
-i multiple locus/germlines, also incomplete/unusual rearrangements (must be used with -g)
-i try to detect incomplete/unusual recombinations (locus with '+', must be used with -g)
-2 try to detect unexpected recombinations (must be used with -g)
- 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 custom V or J repertoires with added sequences.
- The =-g germline/= option launches the analysis on the seven germlines, selecting the best locus for each read.
Using =-g germline/ -i= stests also some incomplete and unusual recombinations (locus with a =+= in their name)
Using =-g germline/ -i= tests also some incomplete and unusual recombinations (locus with a =+= in their name),
and using =-g germline/ -i -2= further test unexpected recombinations.
See [[][]] for information on the analyzable locus.
- Analyzed locus and parameters are configured through the =germline/ file.
To select a custom set of TR or Ig locus, you may copy =germline/ into a new file,
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