about VQSR -- VariantRecalibrator

Dear all, please could you advise on the following : how is more appropriate to set up the VQSR as I have noted some discrepancies between different resource materials ? Here is what I mean :

I. about SNP :

--- in GATK workshop materials (resource:omni ------- truth=false ):

resource:hapmap,known=false,training=true,truth=true,prior=15.0 $HAPMAP33 \
resource:omni,known=false,training=true,truth=false,prior=12.0 $OMNI25 \
resource:1000G,known=false,training=true,truth=false,prior=10.0 $SNP1000G \
resource:dbsnp,known=true,training=false,truth=false,prior=2.0 $DBSNP138 \

--- while in the online documentation (https://software.broadinstitute.org/gatk/guide/article?id=1259)
(resource omni -- truth=true):

resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.sites.vcf \

II. about INDEL :

-- in Current protocols in Bioinfo (resource:mills ------- known=true) :

resource:mills,known=true,training=true,truth=true,prior=12.0 $INDEL1000G \
resource:dbsnp,known=true,training=false,truth=false,prior=2.0 $DBSNP138 \

-- while in the online documentation (https://software.broadinstitute.org/gatk/guide/article?id=1259)
(resource:mills -- known=false):

resource:mills,known=false,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.sites.vcf \

thanks !

bogdan