VCFX_reformatter¶

Overview¶

VCFX_reformatter is a tool for reformatting INFO and FORMAT fields in VCF files. It provides functionality to compress (remove) specific fields and reorder fields in both INFO and FORMAT columns, making VCF files more organized and efficient.

Usage¶

VCFX_reformatter [options] < 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`)
`-c, --compress-info <keys>`	Remove specified INFO keys (comma-separated)
`-f, --compress-format <keys>`	Remove specified FORMAT keys (comma-separated)
`-i, --reorder-info <keys>`	Reorder INFO keys (comma-separated)
`-o, --reorder-format <keys>`	Reorder FORMAT keys (comma-separated)

Description¶

VCFX_reformatter modifies VCF files in several ways:

INFO Field Compression:
Removes specified keys from the semicolon-separated INFO field
Preserves remaining fields in their original order
Handles both key-value pairs and flag fields
FORMAT Field Compression:
Removes specified keys from the colon-separated FORMAT field
Updates all sample columns to match the new FORMAT structure
Maintains data consistency across all samples
INFO Field Reordering:
Places specified keys at the beginning of the INFO field
Appends remaining keys in their original order
Preserves all key-value pairs and flags
FORMAT Field Reordering:
Reorders the FORMAT column keys
Updates all sample columns to match the new order
Maintains data alignment across all samples

Input Requirements¶

Input must be a valid VCF file
File can be piped through stdin
Supports both VCFv4.0 and VCFv4.2 formats
Handles both single-sample and multi-sample VCFs

Output Format¶

The output is a VCF file with: - All header lines preserved - Modified INFO and FORMAT fields according to specifications - Updated sample columns to match new FORMAT structure - Original VCF format maintained

Examples¶

Basic Usage¶

Remove specific INFO fields and reorder others:

VCFX_reformatter --compress-info AF,DP --reorder-info AF,DP < input.vcf > output.vcf

Format Field Manipulation¶

Remove and reorder FORMAT fields:

VCFX_reformatter --compress-format PL,AD --reorder-format GT,DP < input.vcf > output.vcf

Combined Operations¶

Perform multiple operations in one command:

VCFX_reformatter \
  --compress-info AF,DP \
  --compress-format PL,AD \
  --reorder-info AF,DP \
  --reorder-format GT,DP \
  < input.vcf > output.vcf

Integration with Other Tools¶

Combine with other VCFX tools:

cat input.vcf | \
  VCFX_validator | \
  VCFX_reformatter --compress-info AF,DP | \
  VCFX_metadata_summarizer

Field Handling¶

INFO Field Processing¶

Handles key-value pairs (e.g., "DP=10")
Handles flag fields (e.g., "PASS")
Preserves field separators
Maintains field order when specified

FORMAT Field Processing¶

Updates FORMAT column structure
Modifies all sample columns accordingly
Preserves data alignment
Handles missing values (".")

Error Handling¶

The tool handles various error conditions: - Malformed VCF lines - Missing fields - Invalid field formats - Inconsistent sample data - Lines with fewer than 8 columns

Performance Considerations¶

Processes input streamingly
Efficient memory usage
Handles large files
Preserves original data integrity

Limitations¶

Only modifies INFO and FORMAT fields
Does not validate VCF format (use VCFX_validator for validation)
Does not modify other VCF columns
Requires at least 8 columns in data lines

Common Use Cases¶

Removing unnecessary fields to reduce file size
Reordering fields for better readability
Standardizing VCF format across different sources
Preparing VCF files for specific analysis tools
Cleaning up VCF files before processing

Best Practices¶

Validate input VCF before reformatting
Back up original files before modification
Verify output format meets requirements
Use appropriate field combinations
Document field modifications