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.

Best Answer


  • dmittelmandmittelman Posts: 3Member

    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?

  • ebanksebanks Broad InstitutePosts: 689Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin

    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).

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • dmittelmandmittelman Posts: 3Member

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

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