Hello, I am trying to convert my vcf files to fasta. However, after aligning to reference, vcf ID from the header disappears, and bcftools/vcftools are writing only reference seq name in file header. Like > NC_xxxx.1

Any ideas?

I run consensus script like

for file in $inpath/*.vcf ;
do
        echo $file
        bname=$(basename $file)
        echo "base name is $bname"
        bfile=$inpath/$bname".gz"
        outfile=$outpath/$bname".fasta"
        bgzip -c $file > $bfile
        tabix -p vcf $bfile
        cat $reference | vcf-consensus $bfile > $outfile

done