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# EMIT_ALL_CONFIDENT_SITES for Indels?

Member

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.

Tagged:

• Member

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?