Changes

=== 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

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.

== Building an Index for Short Read Alignment ==

== Building an Index for Short Read Alignment ==