Pindel-TD: a tandem duplication detector based on a pattern growth approach

Abstract

Tandem duplication (TD) is a major type of structural variation (SV), and plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most of modern SV detection methods due to the lacking of specialized operation on TD related mutational signals. Herein, we developed a TD detection module of Pindel referred as Pindel-TD based on a TD specific pattern growth approach. Pindel-TD detects TDs with a wide size range at single nucleotide resolution. Using simulation and real read data of HG002, we demonstrate that Pindel-TD outperformed other leading methods in terms of precision, recall, F1-score and robustness. Further applying Pindel-TD on data generated from K562 cancer cell line, we identified a TD located at the seventh exon of SAGE1, explaining its high expression. Pindel-TD is available at https://github.com/xjtu-omics/pindel and free for non-commercial use.