+One minor feature has been implemented in bcftools:
+
+ * Added a reference-free variant calling mode. In this mode, a site is
+ regarded as a variat iff the sample(s) contains two or more alleles;
+ the meaning of the QUAL field in the VCF output is changed
+ accordingly. Effectively, the reference allele is irrelevant to the
+ result in the new mode, although the reference sequence has to be
+ used in realignment when SAMtools computes genotype likelihoods.
+