Update command line doc and examples in README.md
Update command line doc and examples in README.md

bigdatagenomics/adam,bigdatagenomics/adam,laserson/adam,bigdatagenomics/adam,laserson/adam,tdanford/adam,tdanford/adam,laserson/adam,heuermh/adam,heuermh/adam,tdanford/adam,massie/adam,tdanford/adam,massie/adam,massie/adam,heuermh/adam,laserson/adam,bigdatagenomics/adam,massie/adam,heuermh/adam