Ensembl now have a tool called Haplosaurus (still in beta) which will convert your phased VCF into actual protein sequences.
haplo is a local tool implementation of the same functionality that
powers the Ensembl transcript haplotypes view. It takes phased
genotypes from a VCF and constructs a pair of haplotype sequences for
each overlapped transcript; these sequences are also translated into
predicted protein haplotype sequences. Each variant haplotype sequence
is aligned and compared to the reference, and an HGVS-like name is
constructed representing its differences to the reference.
This approach offers an advantage over VEP's analysis, which treats
each input variant independently. By considering the combined change
contributed by all the variant alleles across a transcript, the
compound effects the variants may have are correctly accounted for.
haplo shares much of the same command line functionality with
can use VEP caches, Ensembl databases, GFF and GTF files as sources of
transcript data; all
vep command line flags relating to this
functionality work the same with
Input data must be a VCF containing phased genotype data for at
least one individual; no other formats are currently supported.
When using a VEP cache as the source of transcript annotation, the
first time you run haplo with a particular cache it will spend some
time scanning transcript locations in the cache.
./haplo -i input.vcf -o out.txt -cache