Variant calling

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Data analysis

Call variants

Now that we have reads aligned to the reference genome, let’s call variants using bcftools. Output the variants to the file variants.bcf.

Hint: Check out the bcftools section of the bowtie2 tutorial for an example of how to run bcftools.

Exercise Criteria:

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File variants.bcf exists
File variants.bcf contains the variants
File variants.bcf.csi is the index file of variants.bcf obtained with bcftools index