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Resolve conflict in metrics
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@pichuan @kishwarshafin
pichuan authored and kishwarshafin committed Mar 18, 2024
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Expand Up @@ -8,10 +8,10 @@ Runtime is on HG003 (all chromosomes).

Stage | Time (minutes)
-------------------------------- | ------------------
make_examples | ~107m
call_variants | ~173m
postprocess_variants (with gVCF) | ~30m
total | ~329m = ~5.5 hours
make_examples | ~103m
call_variants | ~196m
postprocess_variants (with gVCF) | ~27m
total | ~326m = ~5.43 hours

### Accuracy

Expand All @@ -23,7 +23,7 @@ held out while training.
| INDEL | 501683 | 2818 | 1265 | 0.994414 | 0.997586 | 0.995998 |
| SNP | 3306788 | 20708 | 4274 | 0.993777 | 0.99871 | 0.996237 |

[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.0/WGS/deepvariant.output.visual_report.html)
[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.1/WGS/deepvariant.output.visual_report.html)

## WES (Illumina)

Expand All @@ -48,7 +48,7 @@ held out while training.
| INDEL | 1022 | 29 | 13 | 0.972407 | 0.987713 | 0.98 |
| SNP | 24987 | 292 | 59 | 0.988449 | 0.997645 | 0.993025 |

[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.0/WES/deepvariant.output.visual_report.html)
[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.1/WES/deepvariant.output.visual_report.html)

## PacBio (HiFi)

Expand All @@ -58,10 +58,10 @@ Runtime is on HG003 (all chromosomes).

Stage | Time (minutes)
-------------------------------- | -------------------
make_examples | ~153m
call_variants | ~195m
make_examples | ~149m
call_variants | ~217m
postprocess_variants (with gVCF) | ~33m
total | ~405m = ~6.75 hours
total | ~399m = ~6.65 hours

### Accuracy

Expand All @@ -76,7 +76,7 @@ to run DeepVariant once.
| INDEL | 501516 | 2985 | 2745 | 0.994083 | 0.994773 | 0.994428 |
| SNP | 3324302 | 3193 | 1502 | 0.99904 | 0.999549 | 0.999295 |

[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.0/PACBIO/deepvariant.output.visual_report.html)
[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.1/PACBIO/deepvariant.output.visual_report.html)

## ONT_R104

Expand All @@ -86,10 +86,10 @@ Runtime is on HG003 reads (all chromosomes).

Stage | Time (minutes)
-------------------------------- | --------------------
make_examples | ~326m
call_variants | ~232m
make_examples | ~329m
call_variants | ~281m
postprocess_variants (with gVCF) | ~34m
total | ~613m = ~10.21 hours
total | ~644m = ~10.73 hours

### Accuracy

Expand All @@ -101,7 +101,7 @@ truth), which was held out while training.
| INDEL | 441658 | 62843 | 41301 | 0.875435 | 0.917411 | 0.895932 |
| SNP | 3314131 | 13364 | 8115 | 0.995984 | 0.997558 | 0.99677 |

[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.0/ONT_R104/deepvariant.output.visual_report.html)
[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.1/ONT_R104/deepvariant.output.visual_report.html)

## Hybrid (Illumina + PacBio HiFi)

Expand All @@ -111,10 +111,10 @@ Runtime is on HG003 (all chromosomes).

Stage | Time (minutes)
-------------------------------- | -------------------
make_examples | ~180m
call_variants | ~178m
postprocess_variants (with gVCF) | ~25m
total | ~406m = ~6.76 hours
make_examples | ~172m
call_variants | ~211m
postprocess_variants (with gVCF) | ~24m
total | ~407m = ~6.78 hours

### Accuracy

Expand All @@ -124,9 +124,9 @@ out while training the hybrid model.
| Type | TRUTH.TP | TRUTH.FN | QUERY.FP | METRIC.Recall | METRIC.Precision | METRIC.F1_Score |
| ----- | -------- | -------- | -------- | ------------- | ---------------- | --------------- |
| INDEL | 503014 | 1487 | 2767 | 0.997053 | 0.994781 | 0.995916 |
| SNP | 3323623 | 3872 | 2273 | 0.998836 | 0.999317 | 0.999077 |
| SNP | 3323624 | 3871 | 2273 | 0.998837 | 0.999317 | 0.999077 |

[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.0/HYBRID/deepvariant.output.visual_report.html)
[See VCF stats report.](https://storage.googleapis.com/deepvariant/visual_reports/DeepVariant/1.6.1/HYBRID/deepvariant.output.visual_report.html)

## Inspect outputs that produced the metrics above

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