FastaAlternateReferenceMakers 4.1.0.0 doesn't give expected output

Hi GATK team,
I run this line:
./gatk FastaAlternateReferenceMakers -R Galaxy47-[ARS-UCD1.2_Btau5.0.1Y.fa.gz].fasta -O Chr20a.SRR4296972.fasta -V Chr20.SRR4296972.g.vcf.gz
But, the tool doesn't change the output fasta based on the vcf file provided.
Here are the screenshots from IGV:
.
The upper part is the BAM file where the vcf coming from, where the below part is the output fasta of FARM.
This variant and with other variants are listed in the vcf file, seen here

hope to hear the solution from you soon,
Thank you,
masagis