Individual filtered VCFs vs filtered standard (variants present in 5/9) samples, `rtg vcfeval -b Shared.vcf.gz -c foo.vcf.gz -t /cm/shared/apps/bcbio/20150720-devel/data/genomes/Hsapiens/GRCh37/rtg/GRCh37.sdf -o eval`:

File  					True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
filtered.Fresh_4706			3338450      54119     339450     0.9840       0.9077     0.9443
filtered.Fresh_4707			3409349     154908     268551     0.9565       0.9270     0.9415
filtered.Fresh_Normal_4708		3464245     190615     213655     0.9478       0.9419     0.9449
filtered.UMFIX_4085			3134462     145638     543438     0.9556       0.8522     0.9010
filtered.UMFIX_4090			3101645     105139     576255     0.9672       0.8433     0.9010
filtered.UMFIX_Normal_4088		3268466     157860     409434     0.9539       0.8887     0.9201
filtered.NBF_4087			3217841     109510     460059     0.9671       0.8749     0.9187
filtered.NBF_4091			3090858     105003     587042     0.9671       0.8404     0.8993
filtered.NBF_Normal_4089		2932151     132203     745749     0.9569       0.7972     0.8698

Repeat with het/hom differences ignored:

File  					True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
filtered.Fresh_4706			3338450      54119     339450     0.9840       0.9077     0.9443
filtered.Fresh_4707			3440339     123918     237561     0.9652       0.9354     0.9501
filtered.Fresh_Normal_4708		3493079     161781     184821     0.9557       0.9497     0.9527
filtered.UMFIX_4085			3167121     112979     510779     0.9656       0.8611     0.9104
filtered.UMFIX_4090			3133905      72879     543995     0.9773       0.8521     0.9104
filtered.UMFIX_Normal_4088		3298795     127531     379105     0.9628       0.8969     0.9287
filtered.NBF_4087			3249176      78175     428724     0.9765       0.8834     0.9276
filtered.NBF_4091			3122006      73855     555894     0.9769       0.8489     0.9084
filtered.NBF_Normal_4089		2960236     104118     717664     0.9660       0.8049     0.8781

Repeat and limit to GiaB high confidence regions:

File  					True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
filtered.Fresh_4706			2457182      30451     231415     0.9878       0.9139     0.9494
filtered.Fresh_4707			2540910      65139     147687     0.9750       0.9451     0.9598
filtered.Fresh_Normal_4708		2590017      90894      98580     0.9661       0.9633     0.9647
filtered.UMFIX_4085			2323935      53437     364662     0.9775       0.8644     0.9175
filtered.UMFIX_4090			2309402      34995     379195     0.9851       0.8590     0.9177
filtered.UMFIX_Normal_4088		2438734      70336     249863     0.9720       0.9071     0.9384
filtered.NBF_4087			2402207      39417     286390     0.9839       0.8935     0.9365
filtered.NBF_4091			2310635      35588     377962     0.9848       0.8594     0.9179
filtered.NBF_Normal_4089		2191893      53634     496704     0.9761       0.8153     0.8885