VCF2GFF

Basic Usage

vcf2gff.sh in=<vcf file> out=<gff file>

VCF2GFF converts Variant Call Format (VCF) files to General Feature Format version 3 (GFF3) files. Each variant call in the VCF becomes a sequence_variant_obs feature in the GFF3 output.

Parameters

VCF2GFF has a minimal parameter set focused on file input/output specification.

Parameters

in=<file>: Input VCF file. Standard VCF format with variant calls to be converted to GFF3 features. Can be compressed (gzip).
out=<file>: Output GFF file. Will be written in GFF3 format with sequence_variant_obs features representing each variant.

Examples

Basic VCF to GFF3 Conversion

vcf2gff.sh in=variants.vcf out=variants.gff3

Converts a VCF file containing variant calls to GFF3 format.

Converting Compressed VCF

vcf2gff.sh in=variants.vcf.gz out=variants.gff3

Processes a gzip-compressed VCF file and outputs uncompressed GFF3.

Pipeline Usage

# Call variants and convert to GFF3
callvariants.sh in=reads.sam ref=reference.fa out=variants.vcf
vcf2gff.sh in=variants.vcf out=variants.gff3

Example pipeline showing variant calling followed by GFF3 conversion for annotation workflows.

Algorithm Details

VCF2GFF implements direct format conversion using the GffLine(VCFLine vcf) constructor, which transforms VCF variant records into standardized GFF3 sequence_variant_obs features through byte-level parsing and coordinate transformation.

Conversion Architecture

Parser Pipeline: VCFLine objects are processed through GffLine constructor with direct field mapping
Coordinate Transformation: VCF 0-based coordinates converted via start=vcf.start()+1; stop=vcf.stop()+1
Strand Assignment: All variants assigned PLUS constant (0) as variants are position-specific, not directional
Source Attribution: Source field set to DOTS constant (".") indicating no specific annotation source

Variant Type Classification

Variant types are determined using vcf.type() and encoded via Var.typeArray[vtype] constants with ByteBuilder string construction:

Substitutions (SUB): bb.append(vcf.ref).append('>').append(vcf.alt) creates "ID=SUB ref>alt"
Insertions (INS): Extracts inserted sequence using vcf.alt, offset, length substring operation
Deletions (DEL): Calculates deletion size via vcf.reflen()-vcf.readlen() producing "ID=DEL length N"
No-calls (NOCALL): Uses vcf.reflen() for uncertain region length in "ID=NOCALL length N"

Quality Score Processing

VCF QUAL values are directly cast to float via score=(float)vcf.qual preserving variant call confidence scores in GFF3 format without transformation or normalization.

Coordinate System Implementation

Coordinate mapping utilizes VCFLine accessor methods with precise boundary calculations:

Start Position: vcf.start()+1 converts 0-based VCF POS to 1-based GFF3 coordinates
End Position: vcf.stop()+1 handles variant span including multi-base substitutions
Span Calculation: Uses Tools.max(v.start+1, v.stop) ensuring valid coordinate ranges

Memory Management

Line-by-line processing using ByteFile input streams with ByteBuilder string manipulation (16-byte initial capacity) minimizes memory footprint. The 200MB heap allocation (-Xmx200m) accommodates VCFLine object instantiation and temporary string construction without requiring full file buffering.

File Format Details

Input VCF Requirements

Standard VCF format (version 4.0 or higher recommended)
Must contain CHROM, POS, REF, ALT, and QUAL fields
Can be compressed with gzip
Headers are processed but not required for conversion

Output GFF3 Format

The output follows GFF3 specification with these characteristics:

Column 1 (seqid): Chromosome/scaffold name from VCF CHROM field
Column 2 (source): Set to "." (no specific source)
Column 3 (type): Always "sequence_variant_obs"
Column 4-5 (start-end): 1-based coordinates of the variant
Column 6 (score): VCF QUAL value (or "." if missing)
Column 7 (strand): Always "+" (plus strand)
Column 8 (phase): Always "." (not applicable to variants)
Column 9 (attributes): Variant type and details encoded as described above

Use Cases

Genome Annotation: Converting variant calls to GFF3 for integration with genome browsers and annotation pipelines
Comparative Genomics: Standardizing variant representations across different analysis tools
Data Exchange: Converting between VCF and GFF3 formats for tools that require specific input formats
Visualization: Preparing variant data for genome browsers that prefer GFF3 format
Annotation Databases: Loading variant information into genomic databases that use GFF3 as their standard format

Support

For questions and support:

Email: bbushnell@lbl.gov
Documentation: bbmap.org