Filtering
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:
$ bcftools query -e'FILTER="."' -f'%CHROM %POS %FILTER\n' file.bcf | head -2 1 3000150 PASS 1 3000151 LowQual
In this example, we use the -i 'QUAL>20 && DP>10' expression to include only sites with big enough quality and depth:
$ bcftools query -i'QUAL>20 && DP>10' -f'%CHROM %POS %QUAL %DP\n' file.bcf | head -2 1 14930 31.2757 13 1 17538 37.9458 12 todo: vcf=/lustre/scratch116/vr/projects/hipsci/cnv/exome-validation/mpileup/ffdm#ffdm_3.bcf $bt query $vcf -i'QUAL="."' -f' %CHROM %POS %QUAL\n' | head -2 Comparing string to numeric value: QUAL="."
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!="."' is not going to work:
$ bcftools query -i'GT!="."' -f'%CHROM %POS [ %GT]\n' file.bcf | head -2 1 30923 ./. 1/1 1 54490 ./. 1/1
Instead, the reverse logic -e 'GT ="."' must be applied:
$ bcftools query -e'GT ="."' -f'%CHROM %POS [ %GT]\n' file.bcf | head -2 1 69511 1/1 1/1 1 71850 0/0 0/1
&& vs & and || vs |)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:
$ bcftools query -i'FMT/DP>10 & FMT/GQ>20' -f'%POS[\t%SAMPLE:DP=%DP GQ=%GQ]\n' file.bcf 49979 SampleA:DP=10 GQ=50 SampleB:DP=20 GQ=40
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 &:
$ bcftools query -i'FMT/DP>10 && FMT/GQ>20' -f'%POS[\t%SAMPLE:DP=%DP GQ=%GQ]\n' file.bcf 31771 SampleA:DP=10 GQ=50 SampleB:DP=40 GQ=20 49979 SampleA:DP=10 GQ=50 SampleB:DP=20 GQ=40
Similarly, the | operator can select just the matching samples:
$ bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' test/view.filter.vcf 3162006 A 19 3162007 A . 3162007 B .
or the whole record when || is used:
$ bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' test/view.filter.vcf 3162006 A 19 3162006 B 1 3162007 A . 3162007 B .
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