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Update case-study docs
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PiperOrigin-RevId: 700115029
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@kishwarshafin @copybara-github
kishwarshafin authored and copybara-github committed Nov 25, 2024
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10 changes: 5 additions & 5 deletions docs/deepvariant-hybrid-case-study.md
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Expand Up @@ -109,7 +109,7 @@ you can run this case study within about half an hour (tested on 64 CPUs).
mkdir -p output
mkdir -p output/intermediate_results_dir

BIN_VERSION="1.7.0"
BIN_VERSION="1.8.0"

sudo docker run \
-v "${PWD}/input":"/input" \
Expand Down Expand Up @@ -182,10 +182,10 @@ Output:
```
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al 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 10628 10602 26 23385 63 12212 10 51 0.997554 0.994361 0.522215 0.995955 NaN NaN 1.748961 2.721448
INDEL PASS 10628 10602 26 23385 63 12212 10 51 0.997554 0.994361 0.522215 0.995955 NaN NaN 1.748961 2.721448
SNP ALL 70166 70138 28 105564 43 35354 16 16 0.999601 0.999388 0.334906 0.999494 2.296566 1.812971 1.883951 2.187440
SNP PASS 70166 70138 28 105564 43 35354 16 16 0.999601 0.999388 0.334906 0.999494 2.296566 1.812971 1.883951 2.187440
INDEL ALL 10628 10601 27 22907 49 11747 9 39 0.997460 0.995609 0.512813 0.996534 NaN NaN 1.748961 2.619528
INDEL PASS 10628 10601 27 22907 49 11747 9 39 0.997460 0.995609 0.512813 0.996534 NaN NaN 1.748961 2.619528
SNP ALL 70166 70145 21 101591 42 31378 12 22 0.999701 0.999402 0.308866 0.999551 2.296566 1.861933 1.883951 2.123073
SNP PASS 70166 70145 21 101591 42 31378 12 22 0.999701 0.999402 0.308866 0.999551 2.296566 1.861933 1.883951 2.123073
```

Notice that F1 scores are above 0.999 for SNPs and above 0.995 for indels!
10 changes: 5 additions & 5 deletions docs/deepvariant-ont-r104-duplex-case-study.md
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Expand Up @@ -75,7 +75,7 @@ mkdir -p "${OUTPUT_DIR}/${INTERMEDIATE_DIRECTORY}"
We will run DeepVariant from docker using the `run_deepvariant` script.

```bash
BIN_VERSION="1.7.0"
BIN_VERSION="1.8.0"

sudo docker run \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
Expand Down Expand Up @@ -153,10 +153,10 @@ Output:
```
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al 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 11256 10306 950 20226 709 8823 343 276 0.915601 0.937823 0.436221 0.926579 NaN NaN 1.561710 2.045850
INDEL PASS 11256 10306 950 20226 709 8823 343 276 0.915601 0.937823 0.436221 0.926579 NaN NaN 1.561710 2.045850
SNP ALL 71333 71274 59 96103 69 24718 36 23 0.999173 0.999033 0.257203 0.999103 2.314904 1.927434 1.715978 1.647902
SNP PASS 71333 71274 59 96103 69 24718 36 23 0.999173 0.999033 0.257203 0.999103 2.314904 1.927434 1.715978 1.647902
INDEL ALL 11256 10372 884 21138 697 9801 364 214 0.921464 0.938520 0.463667 0.929914 NaN NaN 1.561710 2.008049
INDEL PASS 11256 10372 884 21138 697 9801 364 214 0.921464 0.938520 0.463667 0.929914 NaN NaN 1.561710 2.008049
SNP ALL 71333 71304 29 110055 63 38637 19 22 0.999593 0.999118 0.351070 0.999356 2.314904 1.752724 1.715978 1.562169
SNP PASS 71333 71304 29 110055 63 38637 19 22 0.999593 0.999118 0.351070 0.999356 2.314904 1.752724 1.715978 1.562169
```

## Acknowledgement
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10 changes: 5 additions & 5 deletions docs/deepvariant-ont-r104-simplex-case-study.md
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Expand Up @@ -74,7 +74,7 @@ mkdir -p "${OUTPUT_DIR}/${INTERMEDIATE_DIRECTORY}"
We will run DeepVariant from docker using the `run_deepvariant` script.

```bash
BIN_VERSION="1.7.0"
BIN_VERSION="1.8.0"

sudo docker run \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
Expand Down Expand Up @@ -153,10 +153,10 @@ Output:
```
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al 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 10628 9165 1463 18460 934 8010 432 339 0.862345 0.910622 0.433911 0.885826 NaN NaN 1.748961 2.129371
INDEL PASS 10628 9165 1463 18460 934 8010 432 339 0.862345 0.910622 0.433911 0.885826 NaN NaN 1.748961 2.129371
SNP ALL 70166 69925 241 91027 151 20935 82 29 0.996565 0.997846 0.229987 0.997205 2.296566 1.944646 1.883951 1.843331
SNP PASS 70166 69925 241 91027 151 20935 82 29 0.996565 0.997846 0.229987 0.997205 2.296566 1.944646 1.883951 1.843331
INDEL ALL 10628 9408 1220 19574 912 8954 391 305 0.885209 0.914124 0.457444 0.899434 NaN NaN 1.748961 2.269171
INDEL PASS 10628 9408 1220 19574 912 8954 391 305 0.885209 0.914124 0.457444 0.899434 NaN NaN 1.748961 2.269171
SNP ALL 70166 70100 66 103527 50 33353 20 24 0.999059 0.999287 0.322167 0.999173 2.296566 1.773367 1.883951 1.794260
SNP PASS 70166 70100 66 103527 50 33353 20 24 0.999059 0.999287 0.322167 0.999173 2.296566 1.773367 1.883951 1.794260
```

## Acknowledgement
Expand Down

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