Commit bfd232ad authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org, doc/locus.org: help on -g

parent 8fb4438f
......@@ -178,8 +178,10 @@ Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all co
-D <file> D germline multi-fasta file (and resets -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, IGK and IGL and sets window prediction parameters)
-i multiple germlines, also incomplete rearrangements (must be used with -g)
-g <path> multiple locus/germlines. In the path <path>, takes 'germlines.data' 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 'germlines.data' file can also be provided with -g <file>
-i multiple locus/germlines, also incomplete/unusual rearrangements (must be used with -g)
#+END_EXAMPLE
- Options such as =-G germline/IGH= or =-G germline/TRG= select one germline system.
......@@ -188,8 +190,8 @@ Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all co
- 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.
See [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]] for information on the analyzable locus.
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.
Analyzed locus and parameters are configured through the =germline/germlines.data= file.
Other configurations files can be selected, for example with =-g germline/custom-germlines.data -i=.
** Main algorithm parameters
......
......@@ -7,7 +7,7 @@ The Vidjil browser is able to display multi-locus data, as long as this informat
is provided in the =.vidjil= file computed by the analysis program.
The Vidjil algorithm currently analyzes the following locus,
selecting the best locus for each read.
The configuration of analyzed locus is done in the =germline/germlines.data= file.
|----------------------+-------+-------------------------+--------+-----------------------------------|
| | | complete recombinations | | incomplete/special recombinations |
......@@ -34,9 +34,5 @@ The detection of incomplete/special recombinaisons is more challenging and may f
In particular, as D genes may be very short, detecting TRD+ (Dd2/Dd3) and IGH+ (Dh-Jh) recombinations
require to have reads with fairly conserved D genes.
/Development note./
The algorithm parameters are hard-coded for each locus, it is defined in the =algo/core/germline.cpp= files.
In a future release, the mechanism will be more flexible and will parse the =germline/germlines.data= file.
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