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lucasbrambrinkcopybara-github
lucasbrambrink
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Update all DeepTrio case-studies for 1.9 release (including metrics)
PiperOrigin-RevId: 757941033
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‎docs/deeptrio-pacbio-case-study.md‎

Lines changed: 19 additions & 19 deletions
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@@ -85,7 +85,7 @@ is run as a separate command.
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mkdir -p output
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mkdir -p output/intermediate_results_dir
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BIN_VERSION="1.8.0"
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BIN_VERSION="1.9.0"
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sudo apt -y update
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sudo apt-get -y install docker.io
@@ -221,13 +221,13 @@ As a result we should get the following output:
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```bash
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Checking: /output/HG002_trio_merged.vcf.gz
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Family: [HG003 + HG004] -> [HG002]
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188 non-pass records were skipped
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Concordance HG002: F:166225/169750 (97.92%) M:166415/168977 (98.48%) F+M:159575/164659 (96.91%)
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126 non-pass records were skipped
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Concordance HG002: F:173615/180788 (96.03%) M:174179/180845 (96.31%) F+M:165688/177112 (93.55%)
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Sample HG002 has less than 99.0 concordance with both parents. Check for incorrect pedigree or sample mislabelling.
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0/188437 (0.00%) records did not conform to expected call ploidy
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176829/188437 (93.84%) records were variant in at least 1 family member and checked for Mendelian constraints
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10143/176829 (5.74%) records had indeterminate consistency status due to incomplete calls
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6722/176829 (3.80%) records contained a violation of Mendelian constraints
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0/191837 (0.00%) records did not conform to expected call ploidy
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185941/191837 (96.93%) records were variant in at least 1 family member and checked for Mendelian constraints
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7334/185941 (3.94%) records had indeterminate consistency status due to incomplete calls
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12647/185941 (6.80%) records contained a violation of Mendelian constraints
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```
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### Benchmark variant calls against 4.2.1 truth set with hap.py
@@ -289,22 +289,22 @@ sudo docker run \
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```
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Benchmarking Summary for HG002:
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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
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INDEL ALL 11256 11213 43 23405 84 11635 32 45 0.996180 0.992863 0.497116 0.994519 NaN NaN 1.561710 2.151675
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INDEL PASS 11256 11213 43 23405 84 11635 32 45 0.996180 0.992863 0.497116 0.994519 NaN NaN 1.561710 2.151675
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SNP ALL 71333 71305 28 108561 21 37160 14 7 0.999607 0.999706 0.342296 0.999657 2.314904 1.742256 1.715978 1.772847
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SNP PASS 71333 71305 28 108561 21 37160 14 7 0.999607 0.999706 0.342296 0.999657 2.314904 1.742256 1.715978 1.772847
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INDEL ALL 11256 11214 42 23119 78 11356 32 40 0.996269 0.993369 0.491198 0.994817 NaN NaN 1.561710 2.075045
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INDEL PASS 11256 11214 42 23119 78 11356 32 40 0.996269 0.993369 0.491198 0.994817 NaN NaN 1.561710 2.075045
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SNP ALL 71333 71310 23 109529 18 38126 9 9 0.999678 0.999748 0.348090 0.999713 2.314904 1.724732 1.715978 1.611481
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SNP PASS 71333 71310 23 109529 18 38126 9 9 0.999678 0.999748 0.348090 0.999713 2.314904 1.724732 1.715978 1.611481
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297297
Benchmarking Summary for HG003:
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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
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INDEL ALL 10628 10577 51 23776 77 12634 33 43 0.995201 0.993089 0.531376 0.994144 NaN NaN 1.748961 2.332224
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INDEL PASS 10628 10577 51 23776 77 12634 33 43 0.995201 0.993089 0.531376 0.994144 NaN NaN 1.748961 2.332224
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SNP ALL 70166 70143 23 117125 35 46898 13 9 0.999672 0.999502 0.400410 0.999587 2.296566 1.57963 1.883951 1.685873
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SNP PASS 70166 70143 23 117125 35 46898 13 9 0.999672 0.999502 0.400410 0.999587 2.296566 1.57963 1.883951 1.685873
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INDEL ALL 10628 10575 53 23560 71 12427 36 34 0.995013 0.993623 0.527462 0.994317 NaN NaN 1.748961 2.321257
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INDEL PASS 10628 10575 53 23560 71 12427 36 34 0.995013 0.993623 0.527462 0.994317 NaN NaN 1.748961 2.321257
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SNP ALL 70166 70149 17 118416 32 48186 8 11 0.999758 0.999544 0.406921 0.999651 2.296566 1.576658 1.883951 1.697684
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SNP PASS 70166 70149 17 118416 32 48186 8 11 0.999758 0.999544 0.406921 0.999651 2.296566 1.576658 1.883951 1.697684
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Benchmarking Summary for HG004:
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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
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INDEL ALL 11000 10954 46 24235 70 12701 29 36 0.995818 0.993931 0.524077 0.994874 NaN NaN 1.792709 2.351344
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INDEL PASS 11000 10954 46 24235 70 12701 29 36 0.995818 0.993931 0.524077 0.994874 NaN NaN 1.792709 2.351344
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SNP ALL 71659 71617 42 116988 22 45260 11 7 0.999414 0.999693 0.386877 0.999554 2.310073 1.633809 1.878340 1.626369
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SNP PASS 71659 71617 42 116988 22 45260 11 7 0.999414 0.999693 0.386877 0.999554 2.310073 1.633809 1.878340 1.626369
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INDEL ALL 11000 10952 48 23981 61 12453 30 27 0.995636 0.994709 0.519286 0.995172 NaN NaN 1.792709 2.328987
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INDEL PASS 11000 10952 48 23981 61 12453 30 27 0.995636 0.994709 0.519286 0.995172 NaN NaN 1.792709 2.328987
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SNP ALL 71659 71622 37 118880 18 47151 6 8 0.999484 0.999749 0.396627 0.999616 2.310073 1.620779 1.878340 1.616919
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SNP PASS 71659 71622 37 118880 18 47151 6 8 0.999484 0.999749 0.396627 0.999616 2.310073 1.620779 1.878340 1.616919
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```

‎docs/deeptrio-quick-start.md‎

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@@ -32,7 +32,7 @@ documentation on how to build.
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### Get Docker image
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```bash
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BIN_VERSION="1.8.0"
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BIN_VERSION="1.9.0"
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sudo apt -y update
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sudo apt-get -y install docker.io
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[BAM]: http://genome.sph.umich.edu/wiki/BAM
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[BWA]: https://academic.oup.com/bioinformatics/article/25/14/1754/225615/Fast-and-accurate-short-read-alignment-with
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[docker build]: https://docs.docker.com/engine/reference/commandline/build/
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[Dockerfile]: https://github.com/google/deepvariant/blob/r1.8/Dockerfile.deeptrio
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[Dockerfile]: https://github.com/google/deepvariant/blob/r1.9/Dockerfile.deeptrio
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[FASTA]: https://en.wikipedia.org/wiki/FASTA_format
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[VCF]: https://samtools.github.io/hts-specs/VCFv4.3.pdf
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[run_deeptrio.py]: ../scripts/run_deeptrio.py

‎docs/deeptrio-wgs-case-study.md‎

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@@ -82,7 +82,7 @@ command.
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mkdir -p output
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mkdir -p output/intermediate_results_dir
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BIN_VERSION="1.8.0"
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BIN_VERSION="1.9.0"
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sudo docker pull google/deepvariant:deeptrio-"${BIN_VERSION}"
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@@ -211,13 +211,13 @@ As a result we should get the following output:
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```bash
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Checking: /output/HG002_trio_merged.vcf.gz
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Family: [HG003 + HG004] -> [HG002]
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86 non-pass records were skipped
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Concordance HG002: F:138004/139790 (98.72%) M:138049/139959 (98.64%) F+M:134711/138044 (97.59%)
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87 non-pass records were skipped
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Concordance HG002: F:138190/140157 (98.60%) M:138255/140341 (98.51%) F+M:135069/138517 (97.51%)
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Sample HG002 has less than 99.0 concordance with both parents. Check for incorrect pedigree or sample mislabelling.
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0/146134 (0.00%) records did not conform to expected call ploidy
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143783/146134 (98.39%) records were variant in at least 1 family member and checked for Mendelian constraints
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5082/143783 (3.53%) records had indeterminate consistency status due to incomplete calls
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3842/143783 (2.67%) records contained a violation of Mendelian constraints
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0/145514 (0.00%) records did not conform to expected call ploidy
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143324/145514 (98.49%) records were variant in at least 1 family member and checked for Mendelian constraints
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4116/143324 (2.87%) records had indeterminate consistency status due to incomplete calls
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3993/143324 (2.79%) records contained a violation of Mendelian constraints
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```
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### Perform analysis with hap.py against 4.2.1 truth set
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```
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Benchmarking Summary for HG002:
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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
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INDEL ALL 11256 11208 48 21232 13 9579 7 4 0.995736 0.998884 0.451159 0.997308 NaN NaN 1.561710 2.044750
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INDEL PASS 11256 11208 48 21232 13 9579 7 4 0.995736 0.998884 0.451159 0.997308 NaN NaN 1.561710 2.044750
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SNP ALL 71333 71088 245 89034 41 17853 4 3 0.996565 0.999424 0.200519 0.997993 2.314904 2.026055 1.715978 1.717178
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SNP PASS 71333 71088 245 89034 41 17853 4 3 0.996565 0.999424 0.200519 0.997993 2.314904 2.026055 1.715978 1.717178
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INDEL ALL 11256 11208 48 21116 13 9462 7 4 0.995736 0.998885 0.448096 0.997308 NaN NaN 1.561710 2.029690
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INDEL PASS 11256 11208 48 21116 13 9462 7 4 0.995736 0.998885 0.448096 0.997308 NaN NaN 1.561710 2.029690
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SNP ALL 71333 71087 246 88097 37 16924 4 6 0.996551 0.999480 0.192106 0.998014 2.314904 2.038019 1.715978 1.700209
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SNP PASS 71333 71087 246 88097 37 16924 4 6 0.996551 0.999480 0.192106 0.998014 2.314904 2.038019 1.715978 1.700209
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Benchmarking Summary for HG003:
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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
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INDEL ALL 10628 10578 50 21055 24 9997 17 6 0.995295 0.997830 0.474804 0.996561 NaN NaN 1.748961 2.209131
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INDEL PASS 10628 10578 50 21055 24 9997 17 6 0.995295 0.997830 0.474804 0.996561 NaN NaN 1.748961 2.209131
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SNP ALL 70166 69977 189 85399 64 15325 17 8 0.997306 0.999087 0.179452 0.998196 2.296566 2.061752 1.883951 1.846595
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SNP PASS 70166 69977 189 85399 64 15325 17 8 0.997306 0.999087 0.179452 0.998196 2.296566 2.061752 1.883951 1.846595
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INDEL ALL 10628 10576 52 20960 23 9905 19 3 0.995107 0.997919 0.472567 0.996511 NaN NaN 1.748961 2.198304
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INDEL PASS 10628 10576 52 20960 23 9905 19 3 0.995107 0.997919 0.472567 0.996511 NaN NaN 1.748961 2.198304
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SNP ALL 70166 69976 190 85469 55 15402 17 4 0.997292 0.999215 0.180206 0.998253 2.296566 2.058455 1.883951 1.850204
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SNP PASS 70166 69976 190 85469 55 15402 17 4 0.997292 0.999215 0.180206 0.998253 2.296566 2.058455 1.883951 1.850204
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Benchmarking Summary for HG004:
295295
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
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INDEL ALL 11000 10949 51 21433 23 9975 16 5 0.995364 0.997993 0.465404 0.996676 NaN NaN 1.792709 2.280107
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INDEL PASS 11000 10949 51 21433 23 9975 16 5 0.995364 0.997993 0.465404 0.996676 NaN NaN 1.792709 2.280107
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SNP ALL 71659 71445 214 86523 48 14980 8 3 0.997014 0.999329 0.173133 0.998170 2.310073 2.064759 1.878340 1.737322
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SNP PASS 71659 71445 214 86523 48 14980 8 3 0.997014 0.999329 0.173133 0.998170 2.310073 2.064759 1.878340 1.737322
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INDEL ALL 11000 10950 50 21369 24 9909 17 5 0.995455 0.997906 0.463709 0.996679 NaN NaN 1.792709 2.271194
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INDEL PASS 11000 10950 50 21369 24 9909 17 5 0.995455 0.997906 0.463709 0.996679 NaN NaN 1.792709 2.271194
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SNP ALL 71659 71445 214 86684 49 15139 6 6 0.997014 0.999315 0.174646 0.998163 2.310073 2.058081 1.878340 1.740313
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SNP PASS 71659 71445 214 86684 49 15139 6 6 0.997014 0.999315 0.174646 0.998163 2.310073 2.058081 1.878340 1.740313
300+
300301
```

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