VCF format issue

[jodyphelan]

I have found an issue with the vcf format output by pilon. Using bcftools view -c 1 pilon.vcf it complains with the error:

[E::bcf_calc_ac] Incorrect allele ("1") in SAMPLE at Chromosome:767398

This seems to be related to this line in the vcf:

Chromosome      767398  .       C       .       .       Del     DP=0;TD=44;BQ=0;MQ=60;QD=0;BC=0,0,0,0;QP=0,0,0,0;PC=114;IC=0;DC=44;XC=0;AC=2;AF=0.00    GT      1/1

The GT field indicates the alternate is present, but the alternate is set to '.'

Is this valid VCF format?