See also

• The SAM/BAM format is described at http://samtools.github.io/hts-specs/SAMv1.pdf
• You can find an introductory explanation to the SAM format on the Abecassis group wiki page at http://genome.sph.umich.edu/wiki/SAM
• If you really need to get complex statistics from BAM files, Alistair Miles' pysamstats library is your port of call, at https://github.com/alimanfoo/pysamstats
• To convert your raw sequence data to alignment data, you will need an aligner; the most widely used is the bwa (http://bio-bwa.sourceforge.net/)
• Picard (surely a reference to Star Trek: The Next Generation) is the most commonly used tool to clean up BAM files; refer to http://broadinstitute.github.io/picard/
• The technical forum for sequence analysis is SEQanswers (http://seqanswers.com/)
• I would like to repeat the recommendation on Biostars here (which is referred to in the previous recipe); it's a treasure trove of information and has a very friendly community, at http://www.biostars.org/
• If you have the Complete Genomics data, take a look at their FAQ at http://www.completegenomics.com/customer-support/faqs/