VCF v4.3 introduces in section 5.5 a way to represent unspecified alleles and REF-only blocks (blocks that don't have any variants). A symbolic alternate allele \<*> is used to represent this unspecified alternate allele, as in:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample
1 4370 . G <*> . . END=4383 GT:DP:GQ 0/0:25:60
1 4384 . C <*> . . END=4388 GT:DP:GQ 0/0:25:45
1 4389 . T TC,<*> 213.73 . . GT:DP:GQ 0/1:23:99
1 4390 . C <*> . . END=4390 GT:DP:GQ 0/0:26:0
Note that it is possible to specify the \<*> allele in every variant (see 1:4389) but the specification doesn't indicate it is mandatory.
VCF v4.3 introduces in section 5.5 a way to represent unspecified alleles and REF-only blocks (blocks that don't have any variants). A symbolic alternate allele \<*> is used to represent this unspecified alternate allele, as in:
Note that it is possible to specify the \<*> allele in every variant (see 1:4389) but the specification doesn't indicate it is mandatory.