A one class java 6 app that filters and compiles a particular set of files generated by SAMTools to identify variation in patient sample sequences when compared to the reference genome.
LASTZVariantFilter.java compiles to two .class files. To run the program from the command line, type:
java LASTZVariantFilter filepath > filteredfilepath
or
java LASTZVariantFilter directorypath > filteredfilepath
Help (an abbreviated version of this README) is provided with
java LASTZOutputSummariser --help
and when you provide no parameters at all