We simulated haplotypes using msprime for a 50 megabase region for varying number of individuals (fixed parameters: recombination rate 2e-8, mutation rate 2e-8, effective population size 1e4) and concatened pairs of haplotypes together to form diploid genotypes. Decompression times were measured by time zcat <file.bcf> > /dev/null for bcf and using the API for Tachyon and timings for printing fixed-fields were measured as time bcftools view <file.bcf> -GH > /dev/null for bcf and time tachyon view -GH > /dev/null for Tachyon. File sizes are listed in gigabytes (1 GB = 10e9 b) and timings in seconds. All experiments were run on a single CPU.
| Variants | Samples | Filesize (BCF) | Filesize (YON) | Decomp. (BCF) | Decomp. (YON) | Print sites (BCF) | Print sites (YON) |
|---|---|---|---|---|---|---|---|
| 523,842 | 10,000 | 0.53655 | 0.16043 | 44.295 | 1.859 | 28.098 | 0.680 |
| 604,487 | 50,000 | 2.57511 | 0.59032 | 251.682 | 7.077 | 137.200 | 1.609 |
| 639,666 | 100,000 | 5.12134 | 0.99690 | 526.733 | 12.473 | 286.413 | 1.936 |
| 685,363 | 250,000 | 12.64719 | 1.90681 | 1927.011 | 24.671 | 1028.046 | 4.745 |
| 719,754 | 500,000 | 25.08209 | 3.04404 | 4139.424 | 45.247 | 2241.756 | 11.706 |
The following table shows data for the 1000 Genomes Project Phase 3 release (2,504 samples, in megabytes; 1 MB = 1E6 bytes). The uncompressed file size represents the amount of bytes needed to be parsed internally
| Contig | BCF-compressed | BCF-uncompressed | YON-compressed | YON-uncompressed | YON-fold | BCF-fold | Uncompressed-fold |
|---|---|---|---|---|---|---|---|
| 1 | 1004.15 | 33140.9 | 258.842 | 1263.27 | 128.04 | 33.004 | 26.234 |
| 2 | 1084.63 | 36284.2 | 275.986 | 1347.19 | 131.47 | 33.453 | 26.933 |
| 3 | 914.54 | 29883.5 | 229.379 | 1132.73 | 130.28 | 32.676 | 26.382 |
| 4 | 922.15 | 29373.0 | 225.035 | 1146.94 | 130.53 | 31.853 | 25.610 |
| 5 | 817.85 | 26980.8 | 204.648 | 1014.88 | 131.84 | 32.990 | 26.585 |
| 6 | 826.64 | 25743.2 | 201.314 | 1016.07 | 127.88 | 31.142 | 25.336 |
| 7 | 750.82 | 24167.4 | 192.220 | 937.06 | 125.73 | 32.188 | 25.791 |
| 8 | 711.66 | 23554.5 | 180.243 | 884.54 | 130.68 | 33.098 | 26.629 |
| 9 | 556.59 | 18244.0 | 149.945 | 704.78 | 121.67 | 32.778 | 25.886 |
| 10 | 639.80 | 20455.4 | 164.439 | 799.29 | 124.40 | 31.971 | 25.592 |
| 11 | 633.70 | 20728.9 | 159.191 | 783.82 | 130.21 | 32.711 | 26.446 |
| 12 | 613.10 | 19821.2 | 157.542 | 766.12 | 125.82 | 32.330 | 25.872 |
| 13 | 460.82 | 14643.6 | 116.473 | 575.91 | 125.72 | 31.777 | 25.427 |
| 14 | 418.90 | 13604.1 | 108.813 | 525.03 | 125.02 | 32.476 | 25.911 |
| 15 | 378.46 | 12423.5 | 104.407 | 479.29 | 118.99 | 32.826 | 25.921 |
| 16 | 408.44 | 13823.2 | 116.201 | 525.16 | 118.96 | 33.843 | 26.322 |
| 17 | 358.58 | 11934.5 | 100.589 | 459.74 | 118.65 | 33.283 | 25.959 |
| 18 | 360.95 | 11616.7 | 96.252 | 462.71 | 120.69 | 32.184 | 25.106 |
| 19 | 295.92 | 9389.2 | 83.711 | 387.25 | 112.16 | 31.728 | 24.246 |
| 20 | 282.46 | 9288.6 | 77.330 | 364.36 | 120.12 | 32.885 | 25.493 |
| 21 | 180.55 | 5664.7 | 50.263 | 236.30 | 112.70 | 31.374 | 23.972 |
| 22 | 177.18 | 5654.2 | 51.468 | 229.95 | 109.86 | 31.912 | 24.589 |
The following table shows data for the Haplotype Reference Consortium (32,488 whole-genome sequenced samples)
| Contig | BCF-compressed | BCF-uncompressed | YON-compressed | YON-uncompressed | YON_fold | BCF_fold | Uncompressed_fold |
|---|---|---|---|---|---|---|---|
| 1 | 5359.20 | 199628 | 895.46 | 5865.5 | 222.93 | 37.250 | 34.034 |
| 2 | 5855.74 | 220586 | 942.84 | 6242.9 | 233.96 | 37.670 | 35.334 |
| 3 | 4991.04 | 183499 | 796.51 | 5355.0 | 230.38 | 36.766 | 34.266 |
| 4 | 5078.87 | 181268 | 763.12 | 5488.2 | 237.53 | 35.691 | 33.029 |
| 5 | 4533.42 | 168300 | 714.14 | 4861.6 | 235.67 | 37.124 | 34.619 |
| 6 | 4588.08 | 159973 | 692.21 | 4807.6 | 231.10 | 34.867 | 33.275 |
| 7 | 4101.22 | 148866 | 676.84 | 4536.9 | 219.94 | 36.298 | 32.812 |
| 8 | 3902.68 | 145836 | 635.00 | 4224.8 | 229.66 | 37.368 | 34.519 |
| 9 | 3000.07 | 109666 | 555.14 | 3456.6 | 197.55 | 36.554 | 31.727 |
| 10 | 3536.07 | 125972 | 593.09 | 3935.3 | 212.40 | 35.625 | 32.010 |
| 11 | 3476.07 | 125957 | 561.41 | 3689.2 | 224.36 | 36.235 | 34.142 |
| 12 | 3330.20 | 120177 | 556.28 | 3661.9 | 216.04 | 36.087 | 32.819 |
| 13 | 2571.01 | 90091 | 421.10 | 2859.1 | 213.94 | 35.041 | 31.510 |
| 14 | 2270.78 | 82613 | 386.20 | 2496.6 | 213.91 | 36.381 | 33.090 |
| 15 | 1996.39 | 74080 | 379.79 | 2278.8 | 195.05 | 37.107 | 32.508 |
| 16 | 2181.47 | 83319 | 451.09 | 2612.2 | 184.70 | 38.194 | 31.896 |
| 17 | 1874.08 | 70884 | 365.79 | 2153.1 | 193.78 | 37.823 | 32.921 |
| 18 | 2001.76 | 71839 | 364.10 | 2321.1 | 197.31 | 35.888 | 30.950 |
| 19 | 1559.36 | 56480 | 312.13 | 1887.2 | 180.95 | 36.220 | 29.928 |
| 20 | 1573.38 | 57548 | 303.62 | 1878.9 | 189.54 | 36.576 | 30.628 |
| 21 | 986.49 | 34548 | 186.18 | 1221.8 | 185.56 | 35.021 | 28.275 |
| 22 | 953.16 | 34110 | 196.84 | 1156.9 | 173.29 | 35.786 | 29.484 |
