How to generate a consensus sequence from a multi-reference BAM file?
This post on biostars has several suggestions.
THe one that seems most straightforward, starting where you are, is to use vcftools:
cat ref.fa | vcf-consensus file.vcf.gz &gt; out.fa

Based on that I think that you should also be able to solve this problem using alfred and GATK.
If all of these suffer the same problem of needing a single sequence (which I very much doubt that they do), you could split the bam / ref files into multiple files, run whatever consensus workflow, and then combine them again. But that doesn't seem like it should be necessary.
See also this post and this post.