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We'll return to this example data shortly to demonstrate a much more involved tool, GATK, to do the same steps.
Mapping Exercise
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You can also get some quick stats with some linux one-liners on this page; there are more thorough analysis programs built to work with vcf's.
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You can't get gene-context information from bcftools - you have to shift to variant annotation tools to do that.
Side-note on samtools mpileup
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