General
Calling
Tips and Tricks

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.)

Simple example: filtering by fixed columns

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="."
FORMAT columns

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
FORMAT columns and boolean expressions

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
Combining scalar and vector fields

The filter -S. example..

Feedback

We welcome your feedback, please help us improve this page by either opening an issue on github or editing it directly and sending a pull request.