The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at


dmittelmandmittelman Member Posts: 3

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 Member Posts: 3

    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 InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 701 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 -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • dmittelmandmittelman Member Posts: 3

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

Sign In or Register to comment.