The versatile bcftools query command can be used to extract any VCF field. Combined with standard UNIX commands, this gives a powerful tool for quick querying of VCFs.

Below is a list of some of the most common tasks with explanation how it works. For a full list of options, see the manual page.

In this example, the -f option defines the output format. The %POS string indicates that for each VCF line we want the POS column printed. The \n stands for a newline character, a notation commonly used in the world of computer programming. Any characters without a special meaning will be passed as is, so for example see this command and its output below:

Here the $ character precedes the command we typed on the command line and below is the actual output that was printed. The | head -3 part limited the output to the first three lines.

Assuming the INFO/AF tag is present, we can refer to it using %INFO/AF or, if unambiguous, using %AF:

If AF annotation is not present but AN and AC are, we can compute the frequencies on the fly:

Because the AC tag can have multiple comma-separated values, we select the first one using the subscript {0}. The awk outputs the first two fields unchanged and computes the fraction using the third and fourth.

FORMAT tags can be extracted using the square brackets [] operator, which loops over all samples. For example, to print the GT field followed by PL field we can write:

Here we used the tab character \t instead of space for a change. If we wanted to print GTs for all samples first followed by PLs for all samples rather than mixing the two types as above, we could write two bracket operators instead:

Please see the plugin split-vep.