IgCaller

IgCaller is used extensively in immunology research to study B-cell receptor diversity and antibody generation mechanisms. Clinically, it helps identify clonal B-cell expansions, monitor minimal residual disease in leukemias and lymphomas, and analyze antibody responses to vaccines. Additionally, it supports therapeutic antibody development by identifying candidate antibodies from strong immune responses.

It is an open-source tool designed to study human B cell Ig gene rearrangements. According to the documentation, it only supports the human hg19 or hg38 genome as the input reference, so the application of this tool is limited to humans. It requires selecting specific areas of the genome.

I am currently working on nonhuman Ig. I may update with more details later when I work with human Ig.

The basic use only requires the short reads aligned BAM file:

IgCaller -I /path/to/IgCaller/IgCaller_reference_files/ -V hg19 -C ensembl -T /path/to/bams/tumor.bam -N /path/to/bams/normal.bam -R /path/to/reference/genome_hg19.fa -o /path/to/IgCaller/outputs/

• Output: IgCaller returns a set of tab-separated files:
  • tumor_sample_output_filtered.tsv: High confidence rearrangements passing the defined filters.
  • tumor_sample_output_IGH.tsv: File containing all IGH rearrangements.
  • tumor_sample_output_IGK.tsv: File containing all IGK rearrangements.
  • tumor_sample_output_IGL.tsv: File containing all IGL rearrangements.
  • tumor_sample_output_class_switch.tsv: File containing all CSR rearrangements.
  • tumor_sample_output_oncogenic_IG_rearrangements.tsv: File containing all oncogenic IG rearrangements (translocations, deletions, inversions, and gains) identified genome-wide.

More details:
Nadeu, F., Mas-de-les-Valls, R., Navarro, A. et al. IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms. Nature Communications 11, 3390 (2020). https://doi.org/10.1038/s41467-020-17095-7.