An "allele" does not have zygosity...so it cannot be either hetero- or
homozygous. An allele is defined as one of potentially many
possibilities at a given location in a genome (a "locus").
A "locus" can be heterozygous or homozygous (among other things),
meaning it either has two different alleles, or exactly the same two
alleles.
Common SNP terminology is somewhat confusing...based on the acronym one
would expect it to refer to a given allele at a specific position, and
sometimes it does. However, "SNP" is more often used to refer to a
specific base (the "locus") that has multiple possible alleles (for
example, a A or a G).
So a heterozygous indel would be one copy of the specific lesion (an
insertion or a deletion), the other strand lacking that particular
insertion or deletion.
Hopefully that helps, if I didn't understand your question, let me know.
Reference:
http://seqanswers.com/forums/showthread.php?t=1175
Look other:
Frequency of homozygous indels vs heterozygous indels