Analyzed human locus
The Vidjil web application displays multi-locus data, as long as this information
is provided in the
.vidjil file computed by the analysis program.
Vidjil-algo currently analyzes the following locus,
selecting the best locus for each read.
The configuration of analyzed locus is done in the
|complete recombinations||incomplete/special recombinations|
|TRD||Vd-(Dd)-Jd||TRD+||Vd-Dd3, Dd2-(Dd)-Jd, Dd2-Dd3|
The detection of complete recombinations is reliable and should work provided that the reads are long enough (especially the J region).
The detection of incomplete/special recombinaisons is more challenging and may fail in some cases. 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 or up/downstream regions.
-2 command line option and the
multi+inc+xxx server configuration try to
detect unexpected or chimeric recombinations between genes of different germlines or on different
strands (such as PCR dimers or +V/-V recombinations).
These recombinations, tagged as
xxx, can be technological artefacts or unusual biological recombinations.