Most BCFtools commands accept the -i, --include and -e, --exclude options which allow advanced filtering. In the examples below, we demonstrate the usage on the query command because it allows us to show the output in a very compact form using the -f formatting option. (For details about the format, see the Extracting information page.)

Fixed columns such as QUAL, FILTER, INFO are straightforward to filter. In this example, we use the -e 'FILTER="."' expression to exclude sites where FILTER is not set:

In this example, we use the -i 'QUAL>20 && DP>10' expression to include only sites with big enough quality and depth:

When filtering FORMAT tags, the OR logic is applied with multiple samples. For example, if we want to remove sites with an uncalled genotype in any sample, the expression -i 'GT!="mis"' is not going to work:

Instead, the reverse logic -e 'GT="mis"' must be applied:

Note we used bcftools view .. | bcftools query …​ to filter first by site, then format the output. Using the same filtering expression directly with the query command would not work, because query excludes samples that do not satisfy the filtering expression

Say our VCF contains the per-sample depth and genotype quality annotations and we want to include only sites where one or more samples have big enough coverage (DP>10) and genotype quality (GQ>20). The expression -i 'FMT/DP>10 & FMT/GQ>20' selects sites where the conditions are satisfied within the same sample:

On the other hand, if we need to include sites where both conditions met but not necessarily in the same sample, we use the && operator rather than &:

Similarly, the | operator can select just the matching samples:

or the whole record when || is used: