This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
EMIT_ALL_CONFIDENT_SITES for Indels?
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.