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@adthrasher
adthrasher committed Jan 23, 2024
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32 changes: 16 additions & 16 deletions text/data_versioning.md
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Expand Up @@ -188,10 +188,10 @@ Using a confident call set to restrict the comparison causes variants outside th
#### HG002 v2.0.0 vs. v3.0.1 without GIAB confidence set
| 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 | 760 | 756 | 4 | 1,026 | 268 | False | 1 | 25 | 0.995… | 0.739… | 0 | 0.848… | | | 2.892… | 4.115… |
| INDEL | PASS | 760 | 752 | 8 | 769 | 15 | False | 1 | 6 | 0.989… | 0.980… | 0 | 0.985… | | | 2.892… | 2.948… |
| SNP | ALL | 16,924 | 16,912 | 12 | 21,339 | 4,427 | False | 5 | 183 | 0.999… | 0.793… | 0 | 0.884… | 3.088… | 2.806… | 1.282… | 1.474… |
| SNP | PASS | 16,924 | 16,901 | 23 | 16,929 | 28 | False | 5 | 2 | 0.999… | 0.998… | 0 | 0.998… | 3.088… | 3.090… | 1.282… | 1.282… |
| INDEL | ALL | 760 | 756 | 4 | 1,026 | 268 | 0 | 1 | 25 | 0.995… | 0.739… | 0 | 0.848… | | | 2.892… | 4.115… |
| INDEL | PASS | 760 | 752 | 8 | 769 | 15 | 0 | 1 | 6 | 0.989… | 0.980… | 0 | 0.985… | | | 2.892… | 2.948… |
| SNP | ALL | 16,924 | 16,912 | 12 | 21,339 | 4,427 | 0 | 5 | 183 | 0.999… | 0.793… | 0 | 0.884… | 3.088… | 2.806… | 1.282… | 1.474… |
| SNP | PASS | 16,924 | 16,901 | 23 | 16,929 | 28 | 0 | 5 | 2 | 0.999… | 0.998… | 0 | 0.998… | 3.088… | 3.090… | 1.282… | 1.282… |
#### HG004 v2.0.0 vs. v3.0.1 with GIAB confidence set
| 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 |
Expand Down Expand Up @@ -220,10 +220,10 @@ Using a confident call set to restrict the comparison causes variants outside th
#### HG005 v2.0.0 vs. v3.0.1 without GIAB confidence set
| 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 | 775 | 769 | 6 | 1,049 | 276 | False | 1 | 30 | 0.992… | 0.737… | 0 | 0.846… | | | 2.755… | 4.005… |
| INDEL | PASS | 775 | 762 | 13 | 776 | 10 | False | 1 | 6 | 0.983… | 0.987… | 0 | 0.985… | | | 2.755… | 2.752… |
| SNP | ALL | 17,378 | 17,363 | 15 | 22,779 | 5,416 | False | 10 | 263 | 0.999… | 0.762… | 0 | 0.865… | 3.026… | 2.662… | 1.177… | 1.423… |
| SNP | PASS | 17,378 | 17,341 | 37 | 17,391 | 50 | False | 10 | 8 | 0.998… | 0.997… | 0 | 0.997… | 3.026… | 3.025… | 1.177… | 1.178… |
| INDEL | ALL | 775 | 769 | 6 | 1,049 | 276 | 0 | 1 | 30 | 0.992… | 0.737… | 0 | 0.846… | | | 2.755… | 4.005… |
| INDEL | PASS | 775 | 762 | 13 | 776 | 10 | 0 | 1 | 6 | 0.983… | 0.987… | 0 | 0.985… | | | 2.755… | 2.752… |
| SNP | ALL | 17,378 | 17,363 | 15 | 22,779 | 5,416 | 0 | 10 | 263 | 0.999… | 0.762… | 0 | 0.865… | 3.026… | 2.662… | 1.177… | 1.423… |
| SNP | PASS | 17,378 | 17,341 | 37 | 17,391 | 50 | 0 | 10 | 8 | 0.998… | 0.997… | 0 | 0.997… | 3.026… | 3.025… | 1.177… | 1.178… |
#### HG002 v3.0.1 vs `main` with GIAB confidence set
| 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 |
Expand All @@ -236,10 +236,10 @@ Using a confident call set to restrict the comparison causes variants outside th
#### HG002 v3.0.1 vs `main` without GIAB confidence set
| 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 | 764 | 752 | 12 | 1,018 | 265 | False | 2 | 23 | 0.984… | 0.740… | 0 | 0.845… | | | 2.907… | 4.126… |
| INDEL | PASS | 764 | 747 | 17 | 756 | 8 | False | 2 | 5 | 0.978… | 0.989… | 0 | 0.984… | | | 2.907… | 2.942… |
| SNP | ALL | 16,929 | 16,906 | 23 | 21,328 | 4,422 | False | 4 | 184 | 0.999… | 0.793… | 0 | 0.884… | 3.090… | 2.806… | 1.282… | 1.471… |
| SNP | PASS | 16,929 | 16,887 | 42 | 16,926 | 39 | False | 4 | 7 | 0.998… | 0.998… | 0 | 0.998… | 3.090… | 3.091… | 1.282… | 1.282… |
| INDEL | ALL | 764 | 752 | 12 | 1,018 | 265 | 0 | 2 | 23 | 0.984… | 0.740… | 0 | 0.845… | | | 2.907… | 4.126… |
| INDEL | PASS | 764 | 747 | 17 | 756 | 8 | 0 | 2 | 5 | 0.978… | 0.989… | 0 | 0.984… | | | 2.907… | 2.942… |
| SNP | ALL | 16,929 | 16,906 | 23 | 21,328 | 4,422 | 0 | 4 | 184 | 0.999… | 0.793… | 0 | 0.884… | 3.090… | 2.806… | 1.282… | 1.471… |
| SNP | PASS | 16,929 | 16,887 | 42 | 16,926 | 39 | 0 | 4 | 7 | 0.998… | 0.998… | 0 | 0.998… | 3.090… | 3.091… | 1.282… | 1.282… |
#### HG004 v3.0.1 vs `main` with GIAB confidence set
| 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 |
Expand Down Expand Up @@ -268,7 +268,7 @@ Using a confident call set to restrict the comparison causes variants outside th
#### HG005 v3.0.1 vs `main` without GIAB confidence set
| 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 | 769 | 761 | 8 | 1,052 | 287 | False | 1 | 37 | 0.990… | 0.727… | 0 | 0.838… | | | 2.689… | 4.063… |
| INDEL | PASS | 769 | 756 | 13 | 775 | 15 | False | 1 | 9 | 0.983… | 0.981… | 0 | 0.982… | | | 2.689… | 2.779… |
| SNP | ALL | 17,387 | 17,362 | 25 | 22,769 | 5,407 | False | 9 | 266 | 0.999… | 0.763… | 0 | 0.865… | 3.025… | 2.661… | 1.178… | 1.419… |
| SNP | PASS | 17,387 | 17,337 | 50 | 17,382 | 45 | False | 8 | 4 | 0.997… | 0.997… | 0 | 0.997… | 3.025… | 3.024… | 1.178… | 1.176… |
| INDEL | ALL | 769 | 761 | 8 | 1,052 | 287 | 0 | 1 | 37 | 0.990… | 0.727… | 0 | 0.838… | | | 2.689… | 4.063… |
| INDEL | PASS | 769 | 756 | 13 | 775 | 15 | 0 | 1 | 9 | 0.983… | 0.981… | 0 | 0.982… | | | 2.689… | 2.779… |
| SNP | ALL | 17,387 | 17,362 | 25 | 22,769 | 5,407 | 0 | 9 | 266 | 0.999… | 0.763… | 0 | 0.865… | 3.025… | 2.661… | 1.178… | 1.419… |
| SNP | PASS | 17,387 | 17,337 | 50 | 17,382 | 45 | 0 | 8 | 4 | 0.997… | 0.997… | 0 | 0.997… | 3.025… | 3.024… | 1.178… | 1.176… |

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