The runtime and accuracy reported in this page are generated using
n2-standard-96 GCP instances which has the following configuration:
GCP instance type: n2-standard-96
CPUs: 96-core (vCPU)
Memory: 384GiB
GPUs: 0Below are the numbers from an Illumina WGS run.
Dataset details:
Sample: HCC1395
Normal coverage: 50x
Tumor coverage: 60xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 67m1.66s |
| call_variants | 212m35.57s |
| postprocess_variants (no gVCF) | 1m5.76s |
| vcf_stats_report (optional) | 3m6.48s |
| total | 293m38.21s (~4h53m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 1766 1515 251 111 0 0 0.931734 0.918703 0.943231 0.931734 0.857871 0.841004 0.873566 0 0 2875001522 0.087304
1 SNVs 39447 37909 37509 400 1938 0 0 0.950871 0.948705 0.952971 0.950871 0.989448 0.988382 0.990440 0 0 2875001522 0.139130
5 records 41073 39675 39024 651 2049 0 0 0.950113 0.947976 0.952187 0.950113 0.983592 0.982306 0.984807 0 0 2875001522 0.226435
Below are the numbers from an Illumina WES run.
Dataset details:
Sample: HCC1395
Normal coverage: 140x
Tumor coverage: 120xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 9m17.72s |
| call_variants | 4m55.99s |
| postprocess_variants (no gVCF) | 0m5.09s |
| vcf_stats_report (optional) | 0m7.29s |
| total | 18m35.83s |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 48 47 44 3 4 0 0 0.916667 0.813945 0.971215 0.916667 0.936170 0.839363 0.981696 0 0 2875001522 0.001043
1 SNVs 1159 1104 1094 10 65 0 0 0.943917 0.929551 0.956071 0.943917 0.990942 0.983992 0.995334 0 0 2875001522 0.003478
5 records 1207 1151 1138 13 69 0 0 0.942833 0.928664 0.954883 0.942833 0.988705 0.981310 0.993655 0 0 2875001522 0.004522
Below are the numbers from a PacBio run.
Dataset details:
Sample: HCC1395
Normal coverage: 45x
Tumor coverage: 60xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 164m33.85s |
| call_variants | 160m15.53s |
| postprocess_variants (no gVCF) | 1m46.21s |
| vcf_stats_report (optional) | 4m39.58s |
| total | 340m38.03s (~5h40m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 1646 1298 348 328 0 0 0.798278 0.778253 0.817242 0.798278 0.788578 0.768356 0.807786 0 0 2875001522 0.121043
1 SNVs 39447 39090 37282 1808 2165 0 0 0.945116 0.942836 0.947331 0.945116 0.953748 0.951632 0.955796 0 0 2875001522 0.628869
5 records 41073 40736 38580 2156 2493 0 0 0.939303 0.936963 0.941581 0.939303 0.947074 0.944868 0.949216 0 0 2875001522 0.749913
Below are the numbers from a ONT run.
Dataset details:
Sample: HCC1395
Normal coverage: 33x
Tumor coverage: 50xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 120m50.85s |
| call_variants | 342m3.23s |
| postprocess_variants (no gVCF) | 3m34.63s |
| vcf_stats_report (optional) | 9m7.72s |
| total | 484m9.62s (~8h4m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 1240 1027 213 599 0 0 0.631611 0.607948 0.654806 0.631611 0.828226 0.806479 0.848442 0 0 2875001522 0.074087
1 SNVs 39447 31411 30603 808 8844 0 0 0.775800 0.771665 0.779896 0.775800 0.974277 0.972482 0.975984 0 0 2875001522 0.281043
5 records 41073 32651 31630 1021 9443 0 0 0.770092 0.766004 0.774142 0.770092 0.968730 0.966800 0.970576 0 0 2875001522 0.355130
Below are the numbers from a FFPE run.
Dataset details:
Sample: HCC1395
Normal coverage: 50x
Tumor coverage: 90xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 117m18.53s |
| call_variants | 411m54.19s |
| postprocess_variants (no gVCF) | 2m5.70s |
| vcf_stats_report (optional) | 6m7.85s |
| total | 548m32.26s (~9h8m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 1550 1288 262 338 0 0 0.792128 0.771896 0.811321 0.792128 0.830968 0.811701 0.849000 0 0 2875001522 0.091130
1 SNVs 39447 33333 32175 1158 7272 0 0 0.815651 0.811802 0.819455 0.815651 0.965260 0.963253 0.967185 0 0 2875001522 0.402782
5 records 41073 34883 33463 1420 7610 0 0 0.814720 0.810941 0.818455 0.814720 0.959292 0.957181 0.961328 0 0 2875001522 0.493913
Below are the numbers from a FFPE WES run.
Dataset details:
Sample: HCC1395
Normal coverage: 185x
Tumor coverage: 190xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 14m26.69s |
| call_variants | 5m10.49s |
| postprocess_variants (no gVCF) | 0m5.41s |
| vcf_stats_report (optional) | 0m7.46s |
| total | 31m16.63s |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 48 35 30 5 18 0 0 0.625000 0.484005 0.751421 0.625000 0.857143 0.714849 0.943328 0 0 2875001522 0.001739
1 SNVs 1159 962 937 25 222 0 0 0.808456 0.785047 0.830326 0.808456 0.974012 0.962490 0.982693 0 0 2875001522 0.008696
5 records 1207 997 967 30 240 0 0 0.801160 0.777938 0.822940 0.801160 0.969910 0.957906 0.979193 0 0 2875001522 0.010435
Below are the numbers from a WGS tumor-only run.
Dataset details:
Sample: HCC1395
Tumor coverage: 60xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 36m20.64s |
| call_variants | 107m41.56s |
| postprocess_variants (no gVCF) | 1m44.98s |
| vcf_stats_report (optional) | 3m37.17s |
| total | 160m20.35s (~2h40m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 4315 1399 2916 227 0 0 0.860394 0.842912 0.876593 0.860394 0.324218 0.310373 0.338298 0 0 2875001522 1.014260
1 SNVs 39447 59386 36190 23196 3257 0 0 0.917434 0.914687 0.920119 0.917434 0.609403 0.605474 0.613321 0 0 2875001522 8.068170
5 records 41073 63698 37589 26109 3484 0 0 0.915175 0.912452 0.917841 0.915175 0.590113 0.586289 0.593928 0 0 2875001522 9.081386
Below are the numbers from a ONT tumor-only run.
Dataset details:
Sample: HCC1395
Tumor coverage: 50xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 61m31.58s |
| call_variants | 240m40.88s |
| postprocess_variants (no gVCF) | 4m23.34s |
| vcf_stats_report (optional) | 10m16.97s |
| total | 327m5.35s (~3h27m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 2165 945 1220 681 0 0 0.581181 0.557074 0.604999 0.581181 0.436490 0.415695 0.457454 0 0 2875001522 0.424348
1 SNVs 39447 51371 30570 20801 8877 0 0 0.774964 0.770823 0.779065 0.774964 0.595083 0.590833 0.599322 0 0 2875001522 7.235127
5 records 41073 53535 31515 22020 9558 0 0 0.767292 0.763187 0.771360 0.767292 0.588680 0.584507 0.592844 0 0 2875001522 7.659126
Below are the numbers from a PacBio tumor-only run.
Dataset details:
Sample: HCC1395
Tumor coverage: 60xRuntime is all chromosomes. Reported runtime is an average of 5 runs.
| Stage | Time (wall time) |
|---|---|
| make_examples_somatic | 89m18.49s |
| call_variants | 133m52.69s |
| postprocess_variants (no gVCF) | 2m54.10s |
| vcf_stats_report (optional) | 6m10.06s |
| total | 242m29.53s (~4h2m) |
somp.py results
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 1626 2379 1278 1101 348 0 0 0.785978 0.765545 0.805394 0.785978 0.537201 0.517129 0.557181 0 0 2875001522 0.382956
1 SNVs 39447 56874 37768 19106 1679 0 0 0.957437 0.955411 0.959395 0.957437 0.664064 0.660174 0.667938 0 0 2875001522 6.645562
5 records 41073 59253 39046 20207 2027 0 0 0.950649 0.948522 0.952712 0.950649 0.658971 0.655146 0.662780 0 0 2875001522 7.028518
For simplicity and consistency, we report runtime with a CPU instance with 96 CPUs This is NOT the fastest or cheapest configuration.
Use gcloud compute ssh to log in to the newly created instance.
Download and run any of the following case study scripts:
# Get the script.
curl -O https://raw.githubusercontent.com/google/deepvariant/r1.8/scripts/inference_deepsomatic.sh
# WGS
bash inference_deepsomatic.sh --model_preset WGS
# PACBIO
bash inference_deepsomatic.sh --model_preset PACBIO
# ONT
bash inference_deepsomatic.sh --model_preset ONT
# FFPE_WGS
bash inference_deepsomatic.sh --model_preset FFPE_WGS
# FFPE_WES
bash inference_deepsomatic.sh --model_preset FFPE_WES
# WGS_TUMOR_ONLY
bash inference_deepsomatic.sh --model_preset WGS_TUMOR_ONLY
# PACBIO_TUMOR_ONLY
bash inference_deepsomatic.sh --model_preset PACBIO_TUMOR_ONLY
# ONT_TUMOR_ONLY
bash inference_deepsomatic.sh --model_preset ONT_TUMOR_ONLY
Runtime metrics are taken from the resulting log after each stage of DeepSomatic.
The accuracy metrics came from the som.py extension of hap.py program.