Commit 2c737a2c authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/ obscure -f option

parent 64fc37d4
......@@ -367,6 +367,9 @@ The =-3= option launches a CDR3/JUNCTION detection based on the position
of Cys104 and Phe118/Trp118 amino acids. This detection relies on alignment
with gapped V and J sequences, as for instance, for V genes, IMGT/GENE-DB sequences.
The advanced =-f= option sets the parameters used in the comparisons between
the clone sequence and the V(D)J germline genes. The default values should work.
The advanced =-m= option controls the minimum difference of positions between the end
of the V and the start of the J. Note that it is even possible to set =-m -10=
(meaning that V and J could overlap 10 bp). This is the default for VJ recombinations
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