Plot twist

Oups. I forgot to mention that we have a second set of DNA sequencing data, stored in the file morereads.fq 😬

The SNPs you obtained in variants.bcf are only half the puzzle; we’ll need to call variants on the file morereads.fq and merge the VCFs in the correct genomic order so that we can decode the secret message.

To save us some time, here’s a pipeline you can use to perform read alignment and variant calling on that second dataset:

In the next step, we’ll see how to merge variants.bcf and variants2.bcf in the correct genomic order.