VCFX_position_subsetter¶

Overview¶

VCFX_position_subsetter extracts variants from a VCF file that fall within a specified genomic region, allowing for targeted analysis of specific chromosomal segments.

Usage¶

VCFX_position_subsetter --region "CHR:START-END" < input.vcf > filtered.vcf

Options¶

Option	Description
`-r`, `--region <CHR:START-END>`	Required. Genomic region to extract in the format "chromosome:start-end"
`-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`)

Description¶

VCFX_position_subsetter reads a VCF file from standard input and outputs only those variants that fall within the specified genomic region. The tool:

Processes a VCF file line by line
Extracts the chromosome and position from each variant
Compares them to the user-specified region
Retains variants where:
The chromosome matches exactly with the specified chromosome
The position falls within the specified start and end coordinates (inclusive)
Outputs all header lines unchanged
Outputs only variant lines that meet the criteria

This tool is particularly useful for: - Focusing analysis on specific genomic regions of interest - Extracting variants in a gene or regulatory region - Reducing file size by narrowing down to relevant regions - Preparing data for local analysis or visualization

Output Format¶

The output is a standard VCF file containing: - All original header lines from the input VCF - Only the variant records that fall within the specified region - The same format and structure as the original VCF

Examples¶

Basic Usage¶

Extract variants on chromosome 1 between positions 1,000,000 and 2,000,000:

VCFX_position_subsetter --region "chr1:1000000-2000000" < input.vcf > chr1_region.vcf

Small Region¶

Extract variants in a small region, such as a specific exon:

VCFX_position_subsetter --region "chr17:41245000-41245500" < input.vcf > brca1_exon.vcf

Different Chromosome Format¶

Extract variants using a different chromosome naming format (numeric):

VCFX_position_subsetter --region "2:150000-250000" < input.vcf > chr2_region.vcf

Pipeline Integration¶

Use as part of a longer analysis pipeline:

cat input.vcf | VCFX_position_subsetter --region "chrX:5000000-6000000" | another_tool > final_output.vcf

Region Parsing¶

Format Requirements¶

The region must be specified in the format "CHR:START-END" where: - CHR is the chromosome name, exactly as it appears in the VCF - START is the beginning position (inclusive) - END is the ending position (inclusive) - The colon and dash are required separators

For example: chr1:10000-20000, X:50000-100000, 22:30500000-31000000

Coordinate System¶

The position coordinates use the same 1-based system as VCF files, where the first base of a chromosome is position 1.

Handling Special Cases¶

Empty Results¶

If no variants in the input VCF fall within the specified region, the output will contain only the header lines.

Non-Existent Chromosome¶

If the specified chromosome does not exist in the input VCF, the output will contain only header lines.

Invalid Region Format¶

If the region is not properly formatted (missing colon, missing dash, or end smaller than start), an error is reported and no filtering is performed.

Malformed Lines¶

Lines with fewer than 2 columns are skipped with a warning
Lines where the position cannot be parsed as an integer are skipped with a warning
Data lines encountered before the #CHROM header are skipped with a warning

Performance Considerations¶

Processes the VCF file line by line, with minimal memory requirements
No preprocessing or indexing is done
Performance scales linearly with input file size
More efficient for small regions in large files compared to manually parsing

Limitations¶

Can only extract one continuous region at a time
No support for multiple regions in a single run
Cannot extract by gene name or other genomic features directly
Requires exact chromosome name matching
No special handling of complex structural variants that may span region boundaries