From Genome Analysis Wiki
→Reference based chunking
=== Reference based chunking ===
REMARK: this works only with SNPIDs in the chr:pos format, or in other
word, rs numbers are not supported here.
In case you didn't split your data with ChunkChromosome, we highly recommend to run imputation using our reference based chunking method (minimac.
10. 3.12 or newer required)