Sequences and Genomic Features Part 2: SAMtools

In the previous module, we learned how to perform an alignment to a reference genome and explored the resulting SAM/BAM files generated after alignment. We also covered the main properties of these file formats.

Now, let’s dive into SAMtools, a powerful suite of tools that allows us to efficiently manipulate and analyze these data files.

• Sequences and Genomic Features 7: SAMtools I

• Sequences and Genomic Features 8: SAMtools II

Materials

You can use the following files, which are similar to the examples presented in the video.

The files are stored in the following directory on the server:

sam_bam/