BAM parsing with samtools
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Samtools utilities

Sort BAM files

When you align FASTQ files with all current sequence aligners, the alignments produced are in random order with respect to their position in the reference genome. In other words, the BAM file is in the order that the sequences occurred in the input FASTQ files.

samtools view sample.bam | head -n 5

Doing anything meaningful such as calling variants or visualizing alignments in IGV) requires that the BAM is further manipulated. It must be sorted such that the alignments occur in “genome order”. That is, ordered positionally based upon their alignment coordinates on each chromosome.

samtools sort sample.bam -o sample.sorted.bam

Now let’s check the order:

samtools view sample.sorted.bam | head -n 5

Notice anything different about the coordinates of the alignments?

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