Table 2 Performance evaluation of MAC on 10 TCGA tumor samples (LUSC)
From: MAC: identifying and correcting annotation for multi-nucleotide variations
Sample barcode | Num. of input SNVs | Num. of BMs | Size of the largest BM | No Annotation | Annovar | VEP | Snpeff | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Memory (Kb) | Run time (min:sec) | Num. of BMCs | Memory (Kb) | Run time (min:sec) | Num. of BMCs | Memory (Kb) | Run time (min:sec) | Num. of BMCs | Memory (Kb) | Run time (min:sec) | ||||
TCGA-18-3409-01A-01D-0983-08 | 3910 | 303 | 4 | 1123088 | 02:18.1 | 108 | 5185632 | 01:47.5 | 108 | 6701680 | 10:08.5 | 112 | 13766144 | 05:00.4 |
TCGA-22-5473-01A-01D-1632-08 | 944 | 21 | 3 | 652336 | 01:05.9 | 6 | 5180416 | 01:10.1 | 6 | 5017200 | 02:35.5 | 6 | 13654800 | 04:10.1 |
TCGA-33-4566-01A-01D-1441-08 | 1451 | 41 | 3 | 844304 | 01:23.5 | 18 | 5180864 | 01:29.0 | 20 | 5020896 | 03:20.2 | 19 | 13706992 | 04:27.2 |
TCGA-34-5231-01A-21D-1817-08 | 743 | 15 | 4 | 459488 | 00:53.8 | 7 | 5180416 | 00:58.6 | 7 | 5015952 | 02:12.6 | 7 | 13635536 | 03:55.1 |
TCGA-37-5819-01A-01D-1632-08 | 839 | 31 | 2 | 380144 | 00:41.0 | 10 | 5184032 | 00:44.1 | 11 | 5013136 | 02:29.6 | 12 | 13725376 | 03:55.3 |
TCGA-39-5031-01A-01D-1441-08 | 754 | 22 | 3 | 549296 | 00:52.5 | 1 | 5180384 | 00:59.2 | 1 | 5018256 | 02:21.9 | 1 | 13644784 | 03:58.5 |
TCGA-46-3769-01A-01D-0983-08 | 1037 | 29 | 3 | 446448 | 00:41.8 | 13 | 5184032 | 01:04.3 | 13 | 5025968 | 02:26.0 | 13 | 13639456 | 03:49.8 |
TCGA-60-2698-01A-01D-1522-08 | 1396 | 34 | 5 | 1198992 | 02:07.6 | 4 | 5180400 | 02:07.2 | 4 | 5021424 | 03:33.8 | 4 | 13715488 | 04:54.1 |
TCGA-66-2785-01A-01D-1522-08 | 1338 | 44 | 3 | 1101216 | 01:56.5 | 4 | 5180848 | 01:54.0 | 4 | 5025424 | 03:33.9 | 4 | 13731600 | 04:53.6 |
TCGA-85-6561-01A-11D-1817-08 | 984 | 14 | 2 | 602112 | 00:44.0 | 3 | 5180400 | 01:31.6 | 3 | 5016176 | 02:26.3 | 3 | 13637520 | 04:09.9 |