Fig. 1: Overview of IgCaller and Ig loci at short-read WGS level. | Nature Communications

Fig. 1: Overview of IgCaller and Ig loci at short-read WGS level.

From: IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms

Fig. 1

a Bioinformatic steps to fully characterize the rearranged Ig gene from short-read WGS data. IgCaller extracts the rearranged sequences from already aligned reads (BAM file). The output of IgCaller might be used as input to downstream specific programs for a complete Ig annotation. b Schema of the Ig loci at B cell genome level (top) and reference genome level (bottom) for the different loci/rearrangements analyzed by IgCaller. Of note, although the IGK locus is oriented on the negative strand, the IGKV4-1, IGKV5-2, and IGKV genes within the distal cluster are inverted and therefore oriented on the positive strand. Thus, rearrangements involving these IGKV genes are formed through inversions rather than deletions. The WGS reads that cover the rearrangements and are used by IgCaller are depicted in each scenario. White arrows represent the coding strand.

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