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=== Required Software ===
=== Required Software ===
In order to run this exercise, you should have BWA ([http://bio-bwa.sourceforge.net available from Sourceforge]), samtools ([http://samtools.sourceforge.net also from Sourceforge]) and thunderVCF ([[UMAKE|included in the UMAKE pipeline download]]) installed. The examples are tested in in bwa 0.6.1, samtools 0.1.18, TrioCaller 0.1.1. The previous version might be not working at certain steps. We assume all executables are under the folder bin/
In order to run this exercise, you should have BWA ([http://bio-bwa.sourceforge.net available from Sourceforge]), samtools ([http://samtools.sourceforge.net also from Sourceforge]) and thunderVCF ([[UMAKE|included in the UMAKE pipeline download]]) installed. The examples are tested in in bwa 0.6.1, samtools 0.1.18, TrioCaller 0.1.1. The previous version might be not working at certain steps. We assume all executables are under folder bin.
== Building an Index for Short Read Alignment ==
== Building an Index for Short Read Alignment ==
