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Mappers spit out SAM/BAM files as output files. BAM is just a binary format of SAM.
Here is a specification of SAM format SAM specification.
Commonly, SAM files are processed in this order:
1. SAM files are converted into BAM files (samstools view)
2. BAM files are sorted by reference coordinates (samtools sort)
3. Sorted BAM files are indexed (samtools index)
Each step above can be done with commands below
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