Table 3 GATK and CASAVA comparison in diseased Family 2
Pipelines | CASAVA all | GATK all | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | HRC | Â | HRC | ||||||||
| Â | Â | Â | HRC by CASAVA but not by GATK | Â | Â | HRC by GATK but not by CASAVA | ||||||
| Â | Total | Total | Total | GT mismatch by GATK | Absent in GATK | Total | Total | Total | GT mismatch by CASAVA | Absent in CASAVA | ||
Total number of variant | 5192891 | 29522 | 912 | 781 | 131 | 5459725 | 30653 | 2043 | 1499 | 544 | ||
TsTv Ratio | 1.99 | 2.04 | 1.30 | By CASAVA | 1.21 | 2.05 | 1.84 | 2.00 | 1.29 | By CASAVA | 1.37 | 1.09 |
| Â | By GATK | 1.23 | Â | By GATK | 1.37 | Â | ||||||
Mendelian Violation | 416915 | 3 | 1 | By CASAVA | 0 | 1 | 265402 | 8 | 8 | By CASAVA | 1010 | 5 |
| Â | By GATK | 244 | Â | By GATK | 3 | Â | ||||||
Mendelian Violation in affected | 279336 | 0 | 0 | By CASAVA | 0 | 0 | 189043 | 0 | 0 | By CASAVA | 929 | 0 |
| Â | By GATK | 211 | Â | By GATK | 0 | Â | ||||||
Mendelian Violation in unaffected | 267367 | 3 | 1 | By CASAVA | 0 | 1 | 182659 | 8 | 8 | By CASAVA | 257 | 5 |
| Â | By GATK | 82 | Â | By GATK | 3 | Â | ||||||
In dbSNP | 4717672 | 28409 | 738 | Â | 656 | 82 | 4754687 | 29129 | 1458 | Â | 1243 | 215 |
In interGenic | 3152905 | 18780 | 602 | Â | 516 | 86 | 3266794 | 19527 | 1349 | Â | 999 | 350 |
In CDS | 54766 | 339 | 6 | Â | 3 | 3 | 53607 | 359 | 26 | Â | 11 | 15 |
In ‘3 UTR | 64961 | 476 | 4 |  | 4 | 0 | 69395 | 483 | 11 |  | 8 | 3 |
In ‘5 UTR | 15087 | 81 | 0 |  | 0 | 0 | 16635 | 92 | 11 |  | 10 | 1 |
In Intronic | 3484737 | 19668 | 487 | Â | 427 | 60 | 3797577 | 20562 | 1381 | Â | 976 | 405 |
In Non_coding_intronic | 180421 | 931 | 38 | Â | 29 | 9 | 182875 | 972 | 79 | Â | 57 | 22 |
In Exonic | 48608 | 284 | 6 | Â | 3 | 3 | 47577 | 292 | 14 | Â | 7 | 7 |
In Non_coding_exonic | 13960 | 82 | 8 | Â | 8 | 0 | 12525 | 82 | 8 | Â | 7 | 1 |
In Putative Promoter Region | 10932 | 56 | 0 | Â | 0 | 0 | 13801 | 66 | 10 | Â | 10 | 0 |
Non-Synonymous Coding | 16299 | 97 | 4 | Â | 3 | 1 | 15429 | 100 | 7 | Â | 3 | 4 |
Common Variant (1000genome + Q108) | 4693812 | 28034 | 784 |  | 728 | 56 | 5224846 | 29186 | 1936 |  | 1418 | 518 |
Homozygougs Minor Variant in 1000genome | 4089468 | 26162 | 396 | Â | 364 | 32 | 4098301 | 26562 | 796 | Â | 726 | 70 |
Homozygougs Minor Variant in Q108 | 4283672 | 26479 | 663 | Â | 628 | 35 | 4469485 | 27677 | 1861 | Â | 1357 | 504 |
Het (>5%) Variant in 1000genome | 3888895 | 25824 | 386 | Â | 354 | 32 | 3897416 | 26225 | 787 | Â | 717 | 70 |
Het(>5) Variant in Q108 | 4355312 | 27616 | 686 | Â | 674 | 12 | 4900523 | 28852 | 1922 | Â | 1408 | 514 |
Non-Synonymous rare Pain related | 5 | 1 | 0 | Â | 0 | 0 | 5 | 1 | 0 | Â | 0 | 0 |
Pain genes mapped to Non-Synonymous rare variants | 4 | 1 | 0 | Â | 0 | 0 | 4 | 1 | 0 | Â | 0 | 0 |