From Genome Analysis Wiki
''' THIS IS IN THE PROCESS OF BEING UPDATED - CHECK BACK SOON'''
If you are creating a program, you can start with Makefile.src found at statgen/src/.
# Update Makefile.tool for your specific program.
#* You may need settings beyond were set in statgen/src/bam/Makefile.tool. See Makefile.src for what settings you can use.
== Recently Added Capabilities ==
* [[SAM/BAM Convert Sequence|SAM/BAM support conversion between '=' and the base in a sequence]]