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Does setting the -out_mode flag in UnifiedGenotyper differently has different effect when doing VQSR

rkanwarrkanwar Posts: 0Member
edited October 2012 in Ask the GATK team


Does VQSR behave differently when the -out_mode flag in UnifiedGenotyper is set to EMIT_VARIANTS_ONLY as compared to EMIT_ALL_CONFIDENT_SITES. I think by using EMIT_ALL_CONFIDENT_SITES we might give VQSR more information to train the model, but I may be wrong. Can someone please help me with this ? Thanks.

cheers, Rahul

Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin
    Answer ✓

    Hi Rahul,

    Emit all confident sites produces confident reference calls too. But they are ignored by the default VQSR mode (SNPs only) so it shouldn't matter. But they aren't ignored if running in BOTH mode.

    In either case, it's definitely not recommended practice to train off of monomorphic sites as it defeats the purpose of the training.

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