Hi Fong,
Alternative allele means the reference allele in addition to any other conflicting/overlapping candidate indel alleles.
-Chris
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Hi Andrew,
The “other” category means that among the set of indel alleles considered, the posterior probability of any single indel allele conditioned on the read observation is not high (in this case meaning < Q30). The principal is that the read has to uniquely support one allele, so a read which for instance just crosses into a long span of breakend homology is not going to meet this criteria. In this case the “set of indel alleles considered” includes the indel allele, the reference allele, and zero to several overlapping alternate indel alleles (the great majority of the time this will be zero). Hope that helps.
-Chris
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