Genotyping of selected germline adaptive immune system loci using short-read sequencing data

Table 3.

Comparison of ImmunoTyper2 accuracy on HPRC samples as different sequencing depths

Gene type Full 30× 20× Downsampling 10× Downsampling
Precision Recall Precision Recall Precision Recall
IGHV 0.836 0.807 0.822 0.800 0.803 0.766
IGLV 0.954 0.899 0.955 0.899 0.956 0.888
IGKV 0.809 0.722 0.814 0.720 0.814 0.700
TRAV 0.787 0.929 0.781 0.924 0.779 0.906
TRBV 0.872 0.930 0.873 0.929 0.875 0.923
TRGV 0.922 0.832 0.922 0.832 0.931 0.837
TRDV 0.293 0.983 0.289 0.983 0.299 0.983

  • Values are the mean; 30× is complete sequence, and 20× and 10× are downsampled.

This Article

  1. Published in Advance August 5, 2025, doi: 10.1101/gr.280314.124 Genome Res. 35: 2076-2086

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