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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

Hello,

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

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