VCFX_ld_calculator¶

Overview¶

VCFX_ld_calculator calculates pairwise linkage disequilibrium (LD) statistics between genetic variants in a VCF file, expressed as r² values. It can analyze variants across an entire file or within a specified genomic region.

New in v2.0: Extreme-performance optimization with memory-mapped I/O, SIMD-accelerated r² computation, multi-threaded matrix mode, and optional distance-based pruning. Achieves 10-100x speedup over v1.2.

Usage¶

VCFX_ld_calculator [OPTIONS] < input.vcf > ld_output.txt
VCFX_ld_calculator -i input.vcf [OPTIONS] > ld_output.txt

Options¶

Option	Description
`-i`, `--input FILE`	Input VCF file (uses memory-mapping for best performance)
`-r`, `--region <chr:start-end>`	Only compute LD for variants in the specified region
`-w`, `--window <N>`	Window size in variants (default: 1000)
`-d`, `--max-distance <BP>`	Max base-pair distance between pairs (0=unlimited, default: 0)
`-t`, `--threshold <R2>`	Only output pairs with r² >= threshold (default: 0.0)
`-n`, `--threads <N>`	Number of threads for matrix mode (default: auto)
`-m`, `--matrix`	Use matrix mode (O(M²) full pairwise matrix)
`-q`, `--quiet`	Suppress informational messages
`-h`, `--help`	Display help message and exit
`-v`, `--version`	Show program version and exit

Description¶

VCFX_ld_calculator reads a VCF file and computes the pairwise linkage disequilibrium (r²) between genetic variants. Linkage disequilibrium is a measure of the non-random association between alleles at different loci, which is important for understanding genetic structure, identifying haplotype blocks, and designing association studies.

The tool operates as follows:

It reads the VCF file (using memory-mapping if -i is specified)
It collects diploid genotypes for each variant, encoding them as:
0: Homozygous reference (0/0)
1: Heterozygous (0/1 or 1/0)
2: Homozygous alternate (1/1)
-1: Missing data or other scenarios (including multi-allelic variants)
For each pair of variants within the window/region, it computes pairwise r² values using SIMD acceleration
It outputs the LD results (format depends on mode)

Computation Modes¶

Default Mode (Streaming)¶

Uses sliding window with std::deque
Only keeps window most recent variants in memory
Outputs pairs incrementally as they're computed
Memory usage: O(window × samples)
Enables LD analysis of files larger than available RAM

Matrix Mode (`--matrix`)¶

Use --matrix flag for full pairwise matrix output
Multi-threaded computation with --threads option
Loads all variants (in region) into memory
Computes full MxM pairwise r² matrix
Memory usage scales with number of variants
Best for small regions where full matrix is needed

Distance-Based Pruning (`--max-distance`)¶

New in v2.0: Skip pairs beyond a physical distance threshold
Biological justification: LD decays exponentially with distance
Beyond ~1Mb, r² is typically < 0.01
Reduces comparisons by 90-99% while capturing biologically relevant LD

Performance Characteristics¶

v2.0 Optimizations¶

Memory-mapped I/O: Uses mmap() with MADV_SEQUENTIAL | MADV_WILLNEED hints for extreme read performance.
SIMD-accelerated r² computation: Processes 16-32 samples simultaneously using NEON (ARM), AVX2, or SSE2 intrinsics.
Multi-threaded matrix computation: Parallel row computation with work-stealing for optimal CPU utilization.
Zero-allocation parsing: VCF lines parsed using raw pointer arithmetic, eliminating heap allocations.
Compact genotype storage: Uses int8_t instead of int for 4x smaller memory footprint.
Pre-computed statistics: Per-variant sum and variance cached to avoid redundant calculations.
Buffered output: 4MB output buffer with direct write() syscalls for minimal I/O overhead.

Complexity Analysis¶

Mode	Time Complexity	Memory
Streaming	O(n × w × m/32)	O(w × m)
Matrix	O(n² × m/32/T)	O(n × m)

Where: n = variants, w = window, m = samples, T = threads

Benchmark Results¶

Mode	Dataset	Time (v1.2)	Time (v2.0)	Speedup
Streaming	2K variants × 2504 samples	1.13s	~0.2s	5x
Streaming	427K variants × 2504 samples	~10 min	~2 min	5x
Matrix	10K variants × 2504 samples	~32 min	~30s	60x

Memory Usage Examples¶

File Size	Variants	Samples	Matrix Mode	Streaming (w=1000)
100 MB	10,000	500	~40 MB	~4 MB
1 GB	100,000	1,000	~800 MB	~8 MB
4 GB	427,000	2,504	~4 GB	~20 MB
10 GB	1,000,000	2,500	OOM	~20 MB

Output Format¶

Streaming Mode (Pairwise List)¶

#VAR1_CHROM VAR1_POS    VAR1_ID VAR2_CHROM  VAR2_POS    VAR2_ID R2
chr1    100 rs123   chr1    200 rs456   0.8500
chr1    100 rs123   chr1    300 rs789   0.4200
chr1    200 rs456   chr1    300 rs789   0.9100

Matrix Mode¶

#LD_MATRIX_START
Index/Var   chr1:100    chr1:200    chr1:300
chr1:100    1.0000  0.4000  0.2000
chr1:200    0.4000  1.0000  0.6000
chr1:300    0.2000  0.6000  1.0000
#LD_MATRIX_END

Examples¶

File Input Mode (Recommended)¶

Use memory-mapped file I/O for best performance:

VCFX_ld_calculator -i input.vcf > ld_pairs.txt
VCFX_ld_calculator -i input.vcf -w 500 -t 0.2 > ld_pairs.txt

Distance-Based Pruning¶

Skip pairs more than 500kb apart (biology: LD decays with distance):

VCFX_ld_calculator -i input.vcf --max-distance 500000 > ld_pairs.txt

Region-Specific LD¶

Calculate LD only for variants in a specific genomic region:

VCFX_ld_calculator -i input.vcf -r chr1:10000-20000 > ld_pairs.txt

Matrix Mode for Small Regions¶

Get full pairwise matrix with multi-threading:

VCFX_ld_calculator -i input.vcf -m -r chr1:10000-20000 -n 8 > ld_matrix.txt

High LD Pairs Only¶

Output only pairs with r² >= 0.8:

VCFX_ld_calculator -i input.vcf -t 0.8 > high_ld_pairs.txt

Combined Options¶

Streaming mode with region filter, window, threshold, and distance limit:

VCFX_ld_calculator -i input.vcf -r chr1:1000000-2000000 -w 1000 -t 0.5 -d 100000 > ld_pairs.txt

Stdin Mode (Backward Compatible)¶

For piped input or integration with other tools:

cat input.vcf | VCFX_ld_calculator > ld_pairs.txt
cat input.vcf | VCFX_ld_calculator -m > ld_matrix.txt

Handling Special Cases¶

Missing Genotypes: Samples with missing genotypes (./. or .|.) are skipped when calculating LD
Multi-allelic Variants: Genotypes involving alleles beyond reference and first alternate are treated as missing
Single Variant: If only one variant is found, outputs message stating no pairwise LD can be calculated
Empty Region: If no variants found in region, outputs appropriate message
Invalid Region Format: Displays error message with correct format example
Chromosome Boundaries: In streaming mode, the window continues across chromosome boundaries unless distance pruning is enabled

Limitations¶

Only supports biallelic variants; multi-allelic variants are treated as missing data
Requires diploid genotypes; haploid genotypes will be treated as missing data
Assumes standard VCF format with GT field in the FORMAT column
Does not support phased vs. unphased distinction; both "/" and "|" separators are treated the same
No built-in visualization of LD patterns
Window is based on variant count by default; use --max-distance for physical distance filtering

Backward Compatibility¶

Breaking Change in v1.2: Default mode changed from matrix to streaming. - To get matrix output, add --matrix flag - The --streaming flag is deprecated (streaming is now default)

New in v2.0: New options added: - -i/--input for mmap mode - -n/--threads for multi-threaded matrix - -d/--max-distance for distance pruning - -q/--quiet for silent operation

All existing options continue to work as before.