Commit ba7950c2 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/ ambiguous/alternate designations

parent f65d9af5
......@@ -107,21 +107,21 @@ Mixed TRA/TRD recombinations can be encoded with =[TRA+D]=.
Other special cases, such as translocations involving BCL1 or BCL2, should be written now as comments after a =#= character.
* Ambiguous designations
* Ambiguous or alternate designations
On some sequences, several V(D)J designations may be equally acceptable.
A future format will allow to specify these alternatives.
It is advised now to leave a comment in plain English:
These alternate choices can be encoded as =(choice1, choice2)=.
For difficult cases, is advised to further leave a comment in plain English:
# The D/J junction can be seen as 2//7, 3//6, or 4//5
>IGHV3-48*01 0/AA/6 IGHD5-12*01 3//6 IGHJ4*02 [IGH]
>IGHV3-48*01 0/AA/6 IGHD5-12*01 (2//7, 3//6, 4//5) IGHJ4*02 [IGH]
# TRGJ1*01 or TRGJ1*02
>TRGV5*01 TRGJ1*02 [TRG]
>TRGV5*01 (TRGJ1*01, TRGJ1*02) [TRG]
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