BCFtools filter

bcftools filter removes variant records from a VCF or BCF file that do not meet a quality expression. The output is a bgzip-compressed VCF (.vcf.gz) that can be registered in the Data library and passed to downstream tools.

Details

Property	Value
Type	Native tool
Binary	bcftools
Subcommand	filter -i (include mode)

Installation

BCFtools must be installed and available in your system PATH.

macOS (Homebrew)

brew install bcftools

Ubuntu/Debian

sudo apt install bcftools

conda

conda install -c bioconda bcftools

Accepted inputs

Extension	Description
.vcf	Uncompressed VCF
.vcf.gz	Bgzip-compressed VCF
.bcf	Binary call format
.bcf.gz	Compressed BCF

Running BCFtools filter

1. Navigate to Tools → BCFtools filter.
2. Select a VCF or BCF file from your Data library.
3. Choose a preset or write a custom filter expression.
4. Click Run filter.

Liatir runs the selected filter expression and shows the compressed VCF output in the results panel.

Filter expression syntax

The -i flag operates in include mode: only variants that satisfy the expression are kept. Variants that do not match are removed.

Fields

Field	Type	Description
QUAL	float	Phred-scaled variant quality
DP	integer	Total read depth at the site
AF	float	Allele frequency (if present in INFO)
FILTER	string	Filter field value ("PASS", ".", etc.)
TYPE	string	Variant type: "snp", "indel", "mnp", "other"
INFO/DP	integer	Depth from INFO field (same as DP for most callers)
FORMAT/GQ	integer	Genotype quality per sample

Operators

Operator	Meaning
>, <, >=, <=	Numeric comparison
=, ==	Equality
!=	Not equal
&&	Logical AND
||	Logical OR
!	Logical NOT

Preset expressions

Preset	Expression	Use case
PASS only	FILTER="PASS"	Keep only variants that passed the caller's internal filters
QUAL > 20	QUAL>20	Basic quality gate; common minimum for variant analysis
QUAL > 30	QUAL>30	Stricter quality gate
QUAL + depth	QUAL>20 && DP>10	Combined quality and coverage filter
SNPs only	TYPE="snp"	Keep only SNPs, discard indels
Indels only	TYPE="indel"	Keep only indels

Custom examples

# High-confidence SNPs
TYPE="snp" && QUAL>30 && DP>20

# Only PASS variants with allele frequency > 5%
FILTER="PASS" && AF>0.05

# Variants on a specific chromosome (requires region syntax instead)
# Use bcftools view -r chr1 for region filtering

Filter vs Annotate

bcftools filter removes non-matching records from the output entirely. If you want to keep all records but mark the filtered ones (soft-filtering), use bcftools filter without -i/-x and instead use the -s flag to set a FILTER tag. The Liatir implementation uses hard-filtering (-i include mode) for simplicity.

Output

The filtered output is a bgzip-compressed VCF (.vcf.gz). It appears in the results panel with:

• Add to Data — registers the filtered VCF in the Data library for immediate use as input to BCFtools stats, SnpEff, or any downstream step.
• Save as… — copies the file to a location you choose via the system save dialog.

After filtering, run BCFtools stats on the filtered output to verify the Ts/Tv ratio and variant counts are within expected ranges.