BAM parsing with samtools
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Explore BAM files

Scrutinize alignments

The samtools view command is the most versatile tool in the samtools package. It’s main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process.

Let us start by inspecting the first five alignments in our BAM in detail:

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

For each read, can you identify where in the genome the read landed? With what mapping quality? Can you parse what the SAM flags mean? (use )

Finally, let’s visualize the alignments:

Using IGV, can you visually identify reads where the DNA sequence differs from that of the reference?

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