Pindel-TD

Pindel-TD detects tandem duplications, a type of structural variation, with single nucleotide resolution using a TD-specific pattern growth approach.

Key Features:

• TD-Specific Pattern Growth Approach: Pindel-TD implements a pattern growth approach specialized for tandem duplication detection, distinguishing TDs from insertions.
• Wide Size Range Detection: Pindel-TD detects tandem duplications across a wide size range at single nucleotide resolution.
• High Precision and Recall: Pindel-TD outperforms other leading methods in precision, recall, F1-score, and robustness on simulated and real read data from HG002.

Scientific Applications:

• Cancer Genomics: Pindel-TD identified a tandem duplication located at the seventh exon of SAGE1 in K562 cancer cell line data, providing an explanation for its high expression.
• Structural Variation Analysis: Pindel-TD enables accurate detection of tandem duplications for studies of novel gene formation and human diseases.

Methodology:

Pindel-TD uses a TD-specific pattern growth approach as a module integrated with the Pindel tool.