VCF to Multifasta Script (Version 2.0.2)

This script converts VCF files to multifasta format, incorporating population information, ploidy levels, and reference sequences for greater flexibility and accuracy. It can handle compressed VCF files.

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Features

• Support for VCF files (both .vcf and .vcf.gz formats).
• Population-aware multifasta generation.
• Reference sequence integration and validation.
• Filtering options using contig/chromosome lists.
• Random allele selection for heterozygous genotypes.
• Customizable ploidy settings.

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Installation

1. Clone or download the repository containing this script.
2. Ensure Python 3 and the required dependencies are installed:
   • Biopython
   • PyVCF

To install dependencies, run:

pip install biopython
pip install pyvcf

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Usage

Run the script with the following command-line options:

Argument	Description	Required	Default
-v, --vcffile	Input VCF file (.vcf or .vcf.gz).	Required	N/A
-o, --outfolder	Output folder for fasta files.	Required	N/A
-r, --reffasta	Fasta reference file.	Optional	None
-c, --contigslist	Text file with contig or chromosome names.	Optional	All contigs.
-n, --popname	File with individual and population names.	Optional	None
-s, --randomSeed	Random seed for reproducibility.	Optional	Current time.
-p, --ploidy	Ploidy of samples.	Optional	2.
-nw, --hidewarnings	hide warnings messages	Optional	False

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Example command line

Convert a VCF file to multifasta format using ploidy 2 and reference sequences:

python vcf_to_multifasta_v2.py -v data/sample.vcf.gz -o output/ \
                               -r data/reference.fasta \
                               -c data/contigs.txt \
                               -n data/populations.txt \
                               -p 2 -s 12345

If a reference fasta is not provided, the script will generate sequences with "N" for missing positions.

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Output

The script generates multifasta files in the specified output folder. Each file corresponds to a contig/chromosome and contains sequences for individuals, formatted as:

>{gene}|{pop}|{indiv}|allele{anbr}
ACTGACTGACTG...