What does the mean 'EMIT_ALL_CONFIDENT_SITES' in GATK UnifiedGenotyper?
from.. GATK Document
-out_mode,--output_mode specifies which sites to emit; possible values are EMIT_VARIANTS_ONLY (the default), EMIT_ALL_CONFIDENT_SITES (include confident reference sites), or EMIT_ALL_SITES (any callable site regardless of confidence).
I really want to know the meaning of confident reference site.
When I calling with the GATK UnifiedGenotyper EMIT_ALL_CONFIDENT_SITES option in each sample BAM file, Can I distinguish the genotype in each sample? (No call, Ref homo, Alt homo, Hetero)
In other words, I know the some site is no call or ref homo for this purpose.