BAM parsing with samtools
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Samtools utilities

Index BAM files

Indexing a genome sorted BAM file allows one to quickly extract alignments overlapping particular genomic regions. Moreover, indexing is required by genome viewers such as IGV so that the viewers can quickly display alignments in each genomic region to which you navigate.

samtools index sample.sorted.bam

This will create an additional “index” file. List (ls) the contents of the current directory and look for the new index file:

Now, let’s exploit the index to extract alignments from chromosome 20. To do this, we use the samtools view command, which we will give proper treatment in the next section. For now, just do it without understanding. No really. Do it.

samtools view sample.sorted.bam 20:1.4e6-1.5e6 | head -n 5

How many alignments are there in this region?

samtools view -c sample.sorted.bam 20:1.4e6-1.5e6
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