EMIT_ALL_CONFIDENT_SITES for Indels?
Posted in Ask the GATK team | Last updated on


Comments (4)

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.


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