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A set of algorithms and heuristics to identify indels from whole genome resequencing datasets using paired-end reads. indelMINER uses a split-read approach to identify the precise breakpoints for indels of size less than a user specified threshold, and supplements that with a paired-end approach to identify larger variants that are frequently missed with the split-read approach.

Software type:
Command line interface
Restrictions to use:
Input data:
indelMINER relies on a combination of split-read and paired-end read approaches to identify indels from a BAM file for a sample.
Input format:
Output format:
The output is provided in the VCF format along with additional information about the variant, including information about its presence or absence in another sample.
Operating system:
Computer skills:
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  • Aakrosh Ratan <rattan at bx.psu.edu>


Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 506, Wartik Laboratory, University Park 16802, PA, USA

  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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