Builds a joint species+individual demultiplexing VCF from consensus-aligned
data. Takes a species-level VCF, per-species individual VCFs, and chain files
for non-reference species; lifts individual variants to consensus coordinates
and writes a single VCF with one donor column per species×individual combination
for use with demuxlet or vireo.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>