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Vidjil – Analyzed human locus

The Vidjil web application is able to display multi-locus data, as long as this information 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/homo-sapiens.g preset.

complete recombinationsincomplete/special recombinations
TRAVa-Ja
TRBVb-(Db)-JbTRB+Db-Jb
TRDVd-(Dd)-JdTRD+Vd-Dd3, Dd2-Jd, Dd2-Dd3
*TRA+D*Vd-(Dd)-Ja, Dd-Ja
TRGVg-Jg
IGHVh-(Dh)-JhIGH+Dh-Jh
IGLVl-Jl
IGKVk-JkIGK+Vk-KDE, INTRON-KDE
command-line option-g germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGL,IGK-g germline/homo-sapiens.g
server configurationmultimulti+inc

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.

Finally, the -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 +V/-V recombinations). These recombinations, tagged as xxx, can be technological artefacts or unusual biological recombinations.