Update documentation

[fnothaft]

What needs to be documented:

• Coordinate systems
• Transformation algorithms (BQSR, indel realignment, mark dups)
• Schemas vs. models
• Update getting started docs
• Write variant discussion up
• Join algorithms - how/what/why?

[antonkulaga]

One or two tutorials with common use-cases (gene expressions, variant calling) will be extremely useful for newcomers like me ( opened an issue on that #491 )

P.S. Some people choose Adam not because of its super-format or very advanced algorithms, but because they are tired of console tools and want to use reasonable (in other words: not R and not Perl) language for dealing with common genomics tasks like gene expression analyses or variant calling together with mapreduce capabilities (to use at least several machines) and adam looks like the only lib that supports for Scala/Spark (I do not count SparkSeq because I am afraid it is abandoned)

[tdanford]

I'll move the coordinate system page, and the FAQ, into the discussion docs today.

[fnothaft]

Closing in favor of #890, #886, #878, #879, #821, #497.