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MICB 405 Bioinformatics: 2021.22

5 Working with SAMtools and BCFtools Part 2

Slides

You can download the slides for this tutorial below.

Exercise

  1. Create a new alignment using bwa aln.
  2. Do a quick comparison using the SN metrics from samtools stats of the bwa aln BAM and the previous bwa mem BAM. What is one metric that changed the most and why might this be?
  3. Filter the bwa aln alignment in order to only keep reads with a mapping quality above a threshold of your choice.
    • Do a quick side-by-side comparison of coverage of your new and old bwa aln alignments using bwa stats. How does introducing a quality threshold lead to a difference here? Can you explain the pros and cons of filtering by mapping quality in terms of sensitivity and specificity?
    • Choosing an arbitrary area along Bordetella’s single contig, what is one difference you can spot between your new and old bwa aln alignments besides read depth? (Hint: take a look at bit flags and positions, and consult IGV’s coloring scheme.)