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written by Chen Sun<p>I want to process the <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> file created by <a href='http://bio-bwa.sourceforge.net/'>BWA</a>, if it is sorted by the sequence coordinate on reference, it will be …
depends what you want to do with the sam. If a bam is sorted on coordinate, then it can be indexed with 'samtools index' and then you can quickly query a genomic region of the bam using random access instead of starting reading the whole bam from the beginning...