Table 1 Performance comparison of Clair3 and PEPPER Margin DeepVariant (PEPPER) with GATK4.

From: Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing

Tool

Variant type

Precision

Recall

F1-Score

Clair3

Overall

1.000

0.969

0.984

PEPPER

Overall

0.968

0.938

0.952

Clair3

SNP

0.967

1.000

0.983

PEPPER

SNP

1.000

0.966

0.983

Clair3

INDEL

1.000

0.333

0.500

PEPPER

INDEL

0.667

0.667

0.667

  1. The table summarizes the performance metrics of Clair3 and PEPPER in relation to the GATK truth set. It presents overall performance alongside specific metrics for SNPs and INDELs, providing precision, recall, and F1-score values for each variant type.
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