Deleted:How to get most likelihood variants in consensus sequence using bcftools

Question

[Info.shi]

Hi everyone! I have a query regarding the consensus sequence I used the below command to create a consensus sequence.

bcftools mpileup -f ref.fasta mapped.bam -d 80000 | bcftools call -c | vcfutils.pl vcf2fq > cons.fq

If I see a reference sequence it shows "GGGA" as I expected it should be "GGGC" in consensus but I get "GGGA" in the consensus sequence.

I checked the VCF file of that variant is not mentioned for the particular gene but I can't understand why it is like so.

Please kindly advise me!

Thank you!