• Pindel-TD is a novel TD detection module that uses a pattern growth approach specifically optimized for tandem duplications, achieving single-nucleotide resolution across a wide size range.
• In benchmarking on simulated and real HG002 data, Pindel-TD outperforms leading SV detection methods (e.g., Manta, DELLY) in precision, recall, F1-score, and robustness.
• Application to K562 cancer cell line data identified a TD in the seventh exon of SAGE1, linking the duplication to its high expression and demonstrating clinical relevance.
• Pindel-TD is freely available for non-commercial use, providing a specialized tool to address the common misclassification of TDs as insertions.