The snakemake workflow described here generates sequences (for both haplotypes) given a bed file of loci and a VCF file. Optionally, you can also convert the multiline fasta into one line. The image shows the entire bioinformatics pipeline with applications using targeted forensic markers.
The particular application this workflow was used included a VCF file from de novo assembly generated by GIAB team at NIST. However, the snakemake workflow can be broadly applied to any VCF file and loci of interest.
snakemake -s vcf2seq_v2.smk -c32
For dry run, use
snakemake -nps vcf2seq_v2.smk -c32
To look at the summary of the snakemake outputs, use
snakemake -s vc2seq_v2 -c32 --summary