Does setting the -out_mode flag in UnifiedGenotyper differently has different effect when doing VQSR
Posted in Ask the GATK team | Last updated on 2012-10-19 01:14:10

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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

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