VCFX_phase_quality_filter¶

Overview¶

VCFX_phase_quality_filter is a tool for filtering variants based on their phasing quality (PQ) scores in the INFO field. It allows users to specify custom conditions for filtering variants based on their PQ values, supporting various comparison operators.

Usage¶

VCFX_phase_quality_filter --filter-pq "PQ<OP><THRESHOLD>" < input.vcf > output.vcf

Options¶

Option	Description
`-h, --help`	Display help message and exit (handled by `vcfx::handle_common_flags`)
`-v`, `--version`	Show program version and exit (handled by `vcfx::handle_common_flags`)
`-f, --filter-pq`	Condition like 'PQ>30', 'PQ>=20', 'PQ!=10', etc.

Description¶

VCFX_phase_quality_filter reads a VCF file and filters variants based on their phasing quality scores:

Extracts the PQ value from the INFO field of each variant
Applies the specified comparison condition to the PQ value
Keeps variants that satisfy the condition
Discards variants that don't meet the criteria

The tool handles missing or invalid PQ values by treating them as 0.0, ensuring robust processing of incomplete data.

Input Requirements¶

Input must be a valid VCF file
File can be piped through stdin
PQ values should be present in the INFO field (optional)
Supports both VCFv4.0 and VCFv4.2 formats

Output Format¶

The output is a VCF file containing only the variants that satisfy the specified PQ condition: - Preserves all header lines - Maintains original VCF format - Includes only passing variants - Preserves all fields and annotations

Examples¶

Basic Usage¶

Filter variants with PQ > 30:

VCFX_phase_quality_filter --filter-pq "PQ>30" < input.vcf > high_pq.vcf

Different Operators¶

Various comparison operators are supported:

# Keep variants with PQ >= 20
VCFX_phase_quality_filter --filter-pq "PQ>=20" < input.vcf > pq_ge_20.vcf

# Keep variants with PQ <= 15
VCFX_phase_quality_filter --filter-pq "PQ<=15" < input.vcf > pq_le_15.vcf

# Keep variants with PQ != 10
VCFX_phase_quality_filter --filter-pq "PQ!=10" < input.vcf > pq_ne_10.vcf

Integration with Other Tools¶

Combine with other VCFX tools:

cat input.vcf | \
  VCFX_validator | \
  VCFX_phase_quality_filter --filter-pq "PQ>30" | \
  VCFX_metadata_summarizer

Supported Operators¶

The tool supports the following comparison operators: - > - Greater than - >= - Greater than or equal to - < - Less than - <= - Less than or equal to - == - Equal to - != - Not equal to

PQ Value Handling¶

The tool handles PQ values in the following ways: - Extracts PQ values from INFO field (e.g., "PQ=30") - Treats missing PQ values as 0.0 - Handles invalid PQ values gracefully - Supports decimal values

Error Handling¶

The tool handles various error conditions: - Missing --filter-pq argument - Invalid condition syntax - Malformed VCF lines - Missing or invalid PQ values - Invalid comparison operators

Performance Considerations¶

Processes input streamingly
Minimal memory usage
Efficient for both small and large VCF files
No need to load entire file into memory

Limitations¶

Only filters based on PQ values
Does not modify PQ values
Does not validate VCF format (use VCFX_validator for validation)
Treats missing PQ values as 0.0

Common Use Cases¶

Filtering low-quality phasing results
Quality control of phased variants
Selecting high-confidence phased variants
Removing poorly phased variants
Quality-based subsetting of phased data

Best Practices¶

Validate input VCF before filtering
Use appropriate PQ thresholds based on your data
Consider missing PQ values in your analysis
Combine with other quality filters
Document your filtering criteria