SOAPindel

SOAPindel is a software tool designed for indel calling. Indels (insertions and deletions) are a significant source of genetic variation, and detecting them is essential in many genomic analyses. SOAPindel is an innovative approach that exploits the differences between a reference genome and a sequenced sample, which can make it difficult to map reads accurately.

The software tool assigns unmapped reads with a mapped partner to their expected genomic positions and performs de novo assembly on regions with many unmapped reads. This approach allows SOAPindel to resolve homozygous, heterozygous, and complex indels by exhaustive traversal of the de Bruijn graph.

SOAPindel provides a list of candidate indels with quality scores, which enables users to assess the reliability of the detected indels. The software tool has shown similar or better performance for short indels (<10 bp) and higher sensitivity and specificity for long indels than other indel calling software such as Dindel, Pindel, and GATK.

A validation experiment suggests SOAPindel has a false-positive rate of around 10% for long indels (>5 bp) while still providing many more candidate indels than other approaches. This makes SOAPindel a powerful tool for detecting indels, especially long indels, which can be challenging to detect accurately.