Add notes about VCF fed to BEAGLE

python/tests/test_imputation.py

@@ -93,6 +93,11 @@ def get_toy_ts():
 
 
 # BEAGLE 4.1 was run on the toy data set above using default parameters.
+#
+# In the query VCF, the site at position 520,000 was redacted and then imputed.
+# Note that the ancestral allele in the simulated tree sequence is
+# treated as the REF in the VCFs.
+#
 # The following are the forward probability matrices and backward probability
 # matrices calculated when imputing into the third individual above. There are
 # two sets of matrices, one for each haplotype.