This will not apply directly to the vcf file, but using extra annotation from bcftools (assuming you are using it for snp and indel calling):
samtools mpileup -uf reference.fasta alignment.bam | \
bcftools view -cg - | vcfutils.pl vcf2fq > consensus.fastq
After that just convert the fastq into a consensus fasta using seqtk, converting all bases with quality lower than 20 to lowercase
seqtk fq2fa consensus.fastq 20 > consensus.fasta
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