What do you mean "stale"? That your .vcf.gz was "too old"? That seems odd, but I am just a user/whacker of problems. By forum software do you mean the upload system at OpenHuans?
Did this work on you BAM file?
samtools mpileup -u -g -f reference_fasta.fa input_bam_file | bcftools call -vmO z -o filename_out.vcf