EMIT_ALL_CONFIDENT_SITES for Indels?

dmittelman

When I use EMIT_ALL_CONFIDENT_SITES for SNPs, I get an expected very large list of genotypes regardless if the genotypes vary from the reference. When I use the same command line but I switch the model to Indels, I only get a VCF of variant sites. Is the EMIT_ALL_CONFIDENT_SITES option not compatible with Indel discovery?

I'm grateful for any clarification.

ebanks

No, it is not. It's is intended only for SNPs.

dmittelman

Eric thanks for the super fast response. Let me just ask, when calling indels, how do I know which regions are callable but simply not variant from the reference?

ebanks

That's actually (unwittingly) a loaded question around us. I personally believe that this can be inferred from the depth (DP) of a region; although there are enough folks here who disagree with me that it is a problem we do plan on tackling in the future (as discussed in other similar threads, and with no promise as to an ETA).

dmittelman

Eric, thanks. This actually makes perfect sense, it is definitely not straightforward.