1. Summary

In this module you will learn about comparing paired tumor-normal samples to find somatic (non-inherited) mutations. In particular, you will first learn some basic facts about the BAM file formats (and a corresponding file called a SAM file). You then will get some practice at manipulating and “viewing” BAM files using a really useful command-line tool called Samtools. We’ll then explore how Samtools, when combined with another tool called VarScan2, can be used to identify both germline and somatic variations. Lastly, you'll use these tools to find somatic mutations in mitochondrial DNA.

2. Presentation Materials

Click here.

3. Hands-on Exercise(s)

Click here.

4. Associated Materials/Files

bam_files.tar.gz

5. Program/Software requirements

Samtools: http://www.htslib.org/download/

VarScan2: http://dkoboldt.github.io/varscan/

6. Advanced Material

Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, et al. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife. 2014;3. (4371858)

Hertweck K, Dasgupta S. The Landscape of mtDNA Modifications in Cancer: A Tale of Two Cities. Frontiers in Oncology. 2017;7:262.

7. Instructor Notes

This module works well for students who have experience using the terminal. No other computer science or biology background is required.