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October 9, 2015 09:00
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| 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 | |
| ``` |
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