View the variants

Now that we’re done with variant calling, let’s see what these variants look like:

The lines that start with # are header lines that contain metadata about the VCF file. To remove those lines:

There’s a lot of information in VCF files but for our purposes we don’t need most of it, so let’s use bcftools query to subset our output. For example, let’s only show the genomic position, the reference allele and the allele that was called at that position:

The last column (%ALT) contains the SNPs we called, and correspond to the secret message that is encoded into DNA.