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- Which mapper finds more variants?
- Can you figure out how to filter the VCF files on various criteria, like coverage, quality, ... ?
- How many high quality mutations are there in these E. coli samples relative to the reference genome?
- Look at how the reads supporting these variants were aligned to the reference genome in the Integrative Genomics Viewer (IGV). This will be a separate tutorial for tomorrow.
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Other version of samtools
As suggested in the initial introduction, the point of this optional tutorial is to work through getting a different version of samtools to work (the command line expectations, flags, and subcommands (ie bcftools call) were not what they are now in version 0.1.18). To make sure you are starting in the right place:
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