Changes

== Input Data ==

== Input Data ==

To get started, you will need bam files in the standard format [http://samtools.sourceforge.net/SAM1.pdf bam format].

To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format].

 

If you do not have glf files, you can generate them from bam files (bam format also specified in [http://samtools.sourceforge.net/SAM1.pdf glf format bam format]) using the following command line:

 

  samtools pileup -g -T 1 -f ref.fa my.bam > my.glf

== How to Run ==

== How to Run ==

== Important Filters ==

== Important Filters ==