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).

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).

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

$ module avail dindel
-------------------- /usr/local/Modules/3.2.9/modulefiles ----------------------
dindel/1.01(default)

$ module load dindel

$ module list
Currently Loaded Modulefiles:
  1) dindel/1.01

$ module unload dindel

$ module load dindel/1.01

$ module show dindel
-------------------------------------------------------------------
/usr/local/Modules/3.2.9/modulefiles/dindel/1.01:

module-whatis    Sets up dindel 1.01 
prepend-path     PATH /usr/local/apps/dindel/1.01/binaries
-----------------------------------------------------------------

Example

$ module load dindel
$ cd /data/$USER/dindel/run1
$ dindel --analysis getCIGARindels --bamFile sample.bam --outputFile sample.dindel_output --ref ref.fa

http://www.sanger.ac.uk/resources/software/dindel/