Use full Y chromosome reference sequence when writing VCF

[apriha]

Per the Ensembl README (ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/README):

Human has sequenced Y chromosomes and the pseudoautosomal region (PAR)
on the Y is annotated. By definition the PAR region is identical on the
X and Y chromosome. The Y chromosome file contains the Y chromsome
minus these repeated PAR regions i.e. the unique portion of Y.

If writing a VCF that contains Y chromosome PAR SNPs, the full Y chromosome reference sequence needs to be reconstructed using the PAR regions from X in order to determine the reference alleles.