Pindel

Pindel is a software tool for detecting breakpoints of large deletions and medium-sized insertions from paired-end short-read sequencing data. It uses a pattern growth algorithm to identify precise genomic breakpoints by analyzing reads that partially map to the reference genome, including split reads and discordant read pairs. By combining these signals, Pindel infers the structure of structural variants at single-base resolution at the breakpoints.

Inputs to Pindel include aligned sequencing data in BAM format and a reference genome, along with user-specified parameters such as minimum read support and minimum indel size. The program searches for patterns anchored by well-mapped reads and extends these patterns to enumerate candidate breakpoints. The output typically comprises a list of detected deletions and insertions with genomic coordinates, size estimates, and supporting evidence; formats may be tab-delimited reports or VCF-like records depending on the version.

Development and usage: Pindel was introduced to the genomics community as a method for identifying structural variants from short-read data and has been widely used in cancer genomics and population genetics. It is distributed as open-source software and has served as a reference approach for split-read–based breakpoint detection. Limitations include sensitivity to read length and sequencing depth, reduced performance in highly repetitive regions, and substantial computational requirements compared with some newer structural-variant callers. It is commonly used alongside other tools to achieve a more comprehensive set of structural variant calls.