VCFX_fasta_converter¶
Overview¶
VCFX_fasta_converter transforms VCF files into FASTA format, converting variant information into a multiple sequence alignment where each sample's sequence represents its genotypes across all variants.
Usage¶
VCFX_fasta_converter [OPTIONS] < input.vcf > output.fasta
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) |
Description¶
VCFX_fasta_converter converts variant information from VCF format into a multiple sequence alignment in FASTA format. The tool:
- Reads a VCF file with variant data and sample genotypes
- Creates one FASTA entry for each sample in the VCF
- Generates one position in the alignment for each variant in the VCF
- Represents each genotype as a single character:
- Homozygous genotypes (0/0, 1/1, etc.) are represented by the corresponding base
- Heterozygous genotypes (0/1, 1/2, etc.) are represented by IUPAC ambiguity codes when possible
- Complex genotypes (indels, multi-base variants) are represented as 'N'
- Outputs a FASTA file with one sequence per sample, where each position corresponds to a variant in the VCF
This tool is useful for: - Creating alignments for phylogenetic analysis - Visualizing genetic variation across samples - Converting VCF data for use with tools that require FASTA format - Simplifying the representation of genetic variation
Output Format¶
The output is a standard FASTA file with one entry per sample:
>SAMPLE1
AGCTYRMKSW
>SAMPLE2
ATCGYRMNNA
>SAMPLE3
GACTYRSWNN
Each position in the sequence corresponds to a variant in the input VCF, with genotypes encoded as follows: - Homozygous reference (0/0): The reference base (e.g., 'A') - Homozygous alternate (1/1): The alternate base (e.g., 'G') - Heterozygous (0/1): IUPAC ambiguity code (e.g., 'R' for A/G) - Missing genotypes (./.): 'N' - Complex or unrepresentable genotypes: 'N'
Examples¶
Basic Usage¶
./VCFX_fasta_converter < variants.vcf > alignment.fasta
Viewing the Alignment¶
# Convert to FASTA and view with alignment viewer
./VCFX_fasta_converter < variants.vcf > alignment.fasta
aliview alignment.fasta
Building a Phylogenetic Tree¶
# Create a FASTA alignment from VCF and build a tree
./VCFX_fasta_converter < variants.vcf > alignment.fasta
iqtree -s alignment.fasta
IUPAC Ambiguity Codes¶
The tool uses standard IUPAC nucleotide ambiguity codes to represent heterozygous genotypes:
| Code | Bases | Meaning |
|---|---|---|
| R | A/G | puRine |
| Y | C/T | pYrimidine |
| M | A/C | aMino |
| K | G/T | Keto |
| S | C/G | Strong (3 H-bonds) |
| W | A/T | Weak (2 H-bonds) |
| N | Any | aNy base or missing data |
Handling Special Cases¶
- Indels and multi-base variants: Represented as 'N' since they can't be unambiguously encoded as a single nucleotide
- Multi-allelic sites: Processed using the appropriate IUPAC codes when possible
- Phased vs. unphased genotypes: Treated identically (e.g., "0|1" and "0/1" both map to the same IUPAC code)
- Missing genotypes: Represented as 'N' in the output sequence
- Missing GT field: Variants without a genotype field are skipped
- Malformed VCF lines: Skipped with a warning
- Invalid nucleotide combinations: Represented as 'N' when no IUPAC code exists
Performance¶
The converter is optimized for efficiency: - Single-pass processing of the VCF file - Efficient string handling for sequence construction - Scales linearly with the number of variants and samples - Maintains a small memory footprint proportional to the number of samples
Limitations¶
- Cannot represent structural variants, indels, or multi-base substitutions
- Loss of information (quality scores, filters, etc.) from the original VCF
- No support for non-diploid genotypes
- Limited to the standard IUPAC ambiguity codes for representing heterozygosity
- Not suitable for variants with complex ALT alleles
- No option to include position information in the output
- Cannot handle extremely large VCF files due to memory constraints (sequence storage)