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- SAM (Sequence Alignment Map) format specification (pdf)
- sam/bam tools
- samtools - sam/bam conversion, flag filtering, bam sort/index
- Picard - sam/bam utilities that are read-group aware
- Translate SAM file flags - type in a decimal number to see which flags are set
- SAMstat - produces detailed graphical statistics for sam/bam files.
- BEDTools - region overlap, merge, coverage & much more, w/bed, bam, vcf, gff support
- BEDTools user manual (pdf)
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