Skip to content

VCFX_variant_counter

Overview

VCFX_variant_counter is a simple utility tool that counts the total number of valid variants (data lines) in a VCF file. It reads input from standard input, processes each line, and outputs the total count of valid variant records.

Usage

VCFX_variant_counter [OPTIONS] < input.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)
-s, --strict Fail on any data line with fewer than 8 columns

Description

VCFX_variant_counter processes a VCF file by:

  1. Reading the VCF file from standard input
  2. Ignoring all header lines (those starting with #)
  3. For each data line:
  4. Checking if it has at least 8 columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO)
  5. If it has 8 or more columns, counting it as a valid variant
  6. If it has fewer than 8 columns:
    • In strict mode: exiting with an error
    • In normal mode: skipping the line with a warning
  7. Finally, printing the total count of valid variants

This tool is useful for quickly determining the number of variants in a VCF file, which can be helpful for quality control, workflow validation, or simply getting an overview of a dataset's size.

VCF Format Requirements

The tool assumes a standard VCF format where: - Header lines start with # - Data lines have at least 8 tab-separated columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO) - Optional FORMAT and sample columns may follow

Examples

Basic Usage

Count the variants in a VCF file: 

VCFX_variant_counter < input.vcf
Output: 
Total Variants: 1234

Using Strict Mode

Count variants with strict validation (will fail on malformed lines): 

VCFX_variant_counter --strict < input.vcf

Using in a Pipeline

Count variants after filtering: 

cat input.vcf | grep -v "FILTER=FAIL" | VCFX_variant_counter

Error Handling

Invalid Lines

  • In normal mode (default):
  • Lines with fewer than 8 columns are skipped
  • A warning is printed to standard error for each skipped line

  • The count continues with valid lines

  • In strict mode (--strict):

  • If any line has fewer than 8 columns, the program exits with an error
  • The error message includes the line number
  • The exit code is 1 to indicate failure

Empty Lines

Empty lines are ignored and not counted.

Performance Considerations

  • The tool processes the VCF file line by line, with minimal memory requirements
  • It performs only basic parsing and doesn't validate the content of each field
  • Performance scales linearly with the number of lines in the input file
  • No external dependencies or reference files are required

Limitations

  • The tool only checks the number of columns, not their content
  • It doesn't validate if the VCF follows the specification for field formats
  • No specific handling for compressed files (use external tools like zcat)
  • No detailed reporting (e.g., breakdown by chromosome or variant type)
  • Cannot handle VCF files with non-standard line endings