SOAPstreaming-Dindel

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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.

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Readme

Source code