VCF2FAS: Converts VCF file(s) to fasta format.
Author: B. Nevado
Usage: vcf2fas -reference reference.fas -vcfs samples.txt -reference: reference genome/transcriptome used. -vcfs: text file with path to vcf files to use. -gf: which field to use for genotypes: GT or PL. -strictIUPAC: if set to 0, errors in assigning IUPAC codes will not crash program (maybe useful for debugging?).
Ouput: 1 fasta file per contig named 'contig_name.fas' to current folder.
Requirements: BIO++ (bio-core and bio-seq v 2.4.0) VCF files must be obtained with SAMtools v1.0+, and filtered with bcftools (should contain 'PASS' for confident variants). Reference homozygous calls can be present.
Notes: INDELS are ignored. Heterozygous genotypes are coded with IUPAC. Only tested with vcf files obtained with SAMtools v1+.
Installation (Linux):
git clone https://github.com/brunonevado/vcf2fas.git
cd vcf2fas
make
./vcf2fas
Installation (Linux / Mac):
If bpp-core and bpp-seq libraries are installed and available on PATH, this should work (from within /source):
g++ -O3 -std=c++11 *cpp -lbpp-core -lbpp-seq -o vcf2fas