Dindel: Accurate indel calls from short-read data

Dindel is a program for calling small indels from short-read sequence data ('next generation sequence data'). It is currently designed to handle only Illumina data.

Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Please see the Dindel manual for the full range of features.

[Genome Research Limited]


Dindel requires a BAM file containing the read-alignments as input. It then extracts candidate indels from the BAM file, and realigns the reads to candidate haplotypes consisting of these candidate indels in windows of ~120 bp. If there is sufficient evidence for an alternative haplotype to the reference, it will call an indel.

Dindel can test candidate indels discovered with other methods, for instance longer deletions found by split-read methods or indels obtained through assembly methods. Dindel will then realign both mapped and unmapped reads to see if the candidate indel is supported by the reads.

Dindel produces a VCF file with the indel calls. Genotype likelihoods can be obtained from intermediate files generated by Dindel.

There is basic support for outputting a realigned BAM file for each realignment-window. These realigned BAM files can be used to call SNPs near (candidate) indels. See the manual for details.

This program was developed by Cornelis Albers together with Gerton Lunter (Wellcome Trust Centre for Human Genetics, University of Oxford) and Richard Durbin (Wellcome Trust Sanger Institute).

For questions, please email Cornelis Albers.


  • Dindel: Accurate indel calls from short-read data.

    CA Albers, G Lunter, Daniel G MacArthur, Gilean McVean, Willem H Ouwehand, Richard Durbin

    Genome Research 2010


Installing Dindel

The Dindel manual explains how to install and run the program on your computer.


* quick link - http://q.sanger.ac.uk/h85ocvbo