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Update case studies and quickstart doc.
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PiperOrigin-RevId: 243160494
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@gunjanbaid
gunjanbaid authored and Copybara-Service committed Apr 11, 2019
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16 changes: 8 additions & 8 deletions docs/deepvariant-case-study.md
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Expand Up @@ -86,17 +86,17 @@ machine, and the `postprocess_variants` step is single-process, single-thread.

With the example in [run_wgs_case_study_docker.sh] on a [CPU machine],

Step | Hardware | Wall time
---------------------------------- | ------------------- | ---------
`make_examples` | 64 CPUs | ~ 1h 10m
`call_variants` | 64 CPUs | ~ 2h 45m
`postprocess_variants` (with gVCF) | 1 CPU | ~ 30m
Step | Hardware | Wall time
---------------------------------- | -------- | ---------
`make_examples` | 64 CPUs | ~ 1h 10m
`call_variants` | 64 CPUs | ~ 2h 45m
`postprocess_variants` (with gVCF) | 1 CPU | ~ 35m

With the example in [run_wgs_case_study_docker_gpu.sh] on a [GPU machine],

Step | Hardware | Wall time
---------------------------------- | ------------------- | ---------
`make_examples` | 16 CPUs | ~ 3h 45m
`make_examples` | 16 CPUs | ~ 3h 25m
`call_variants` | 1 P100 GPU, 16 CPUs | ~ 50m
`postprocess_variants` (with gVCF) | 1 CPU | ~ 30m

Expand Down Expand Up @@ -154,8 +154,8 @@ results.

Type | # FN | # FP | Recall | Precision | F1\_Score
----- | ---- | ---- | -------- | --------- | ---------
INDEL | 1428 | 924 | 0.996927 | 0.998089 | 0.997508
SNP | 1328 | 749 | 0.999564 | 0.999754 | 0.999659
INDEL | 1488 | 944 | 0.996798 | 0.998048 | 0.997423
SNP | 1576 | 725 | 0.999483 | 0.999762 | 0.999623

[install_nvidia_docker.sh]: https://github.com/google/deepvariant/blob/r0.8/scripts/install_nvidia_docker.sh
[run_wgs_case_study_docker.sh]: https://github.com/google/deepvariant/blob/r0.8/scripts/run_wgs_case_study_docker.sh
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4 changes: 2 additions & 2 deletions docs/deepvariant-exome-case-study.md
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Expand Up @@ -110,8 +110,8 @@ We evaluate against the capture region:

Type | # FN | # FP | Recall | Precision | F1\_Score
----- | ---- | ---- | -------- | --------- | ---------
INDEL | 106 | 49 | 0.959231 | 0.980897 | 0.969943
SNP | 48 | 16 | 0.998577 | 0.999525 | 0.999051
INDEL | 117 | 55 | 0.955000 | 0.978507 | 0.966611
SNP | 37 | 23 | 0.998903 | 0.999318 | 0.999110

[specific machine type]: deepvariant-details.md#commands-for-requesting-machines-used-in-case-studies
[install_nvidia_docker.sh]: https://github.com/google/deepvariant/blob/r0.8/scripts/install_nvidia_docker.sh
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8 changes: 4 additions & 4 deletions docs/deepvariant-quick-start.md
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Expand Up @@ -171,10 +171,10 @@ You should see output similar to the following.
```
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 4 4 0 13 0 9 0 1 1 0.692308 1 NaN NaN 0.333333 1.000000
INDEL PASS 4 4 0 13 0 9 0 1 1 0.692308 1 NaN NaN 0.333333 1.000000
SNP ALL 44 44 0 60 0 16 0 1 1 0.266667 1 1.2 1.307692 0.333333 0.363636
SNP PASS 44 44 0 60 0 16 0 1 1 0.266667 1 1.2 1.307692 0.333333 0.363636
INDEL ALL 4 4 0 13 0 9 0 1.000000 1 0.692308 1.000000 NaN NaN 0.333333 1.000000
INDEL PASS 4 4 0 13 0 9 0 1.000000 1 0.692308 1.000000 NaN NaN 0.333333 1.000000
SNP ALL 44 43 1 59 0 16 0 0.977273 1 0.271186 0.988506 1.2 1.36 0.333333 0.340909
SNP PASS 44 43 1 59 0 16 0 0.977273 1 0.271186 0.988506 1.2 1.36 0.333333 0.340909
```

[BAM]: http://genome.sph.umich.edu/wiki/BAM
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