diff --git a/docs/deepvariant-hybrid-case-study.md b/docs/deepvariant-hybrid-case-study.md index 39a0e999..85636997 100644 --- a/docs/deepvariant-hybrid-case-study.md +++ b/docs/deepvariant-hybrid-case-study.md @@ -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 "${PWD}/input":"/input" \ @@ -182,10 +182,10 @@ Output: ``` Benchmarking Summary: Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio -INDEL ALL 10628 10602 26 23385 63 12212 10 51 0.997554 0.994361 0.522215 0.995955 NaN NaN 1.748961 2.721448 -INDEL PASS 10628 10602 26 23385 63 12212 10 51 0.997554 0.994361 0.522215 0.995955 NaN NaN 1.748961 2.721448 - SNP ALL 70166 70138 28 105564 43 35354 16 16 0.999601 0.999388 0.334906 0.999494 2.296566 1.812971 1.883951 2.187440 - SNP PASS 70166 70138 28 105564 43 35354 16 16 0.999601 0.999388 0.334906 0.999494 2.296566 1.812971 1.883951 2.187440 +INDEL ALL 10628 10601 27 22907 49 11747 9 39 0.997460 0.995609 0.512813 0.996534 NaN NaN 1.748961 2.619528 +INDEL PASS 10628 10601 27 22907 49 11747 9 39 0.997460 0.995609 0.512813 0.996534 NaN NaN 1.748961 2.619528 + SNP ALL 70166 70145 21 101591 42 31378 12 22 0.999701 0.999402 0.308866 0.999551 2.296566 1.861933 1.883951 2.123073 + SNP PASS 70166 70145 21 101591 42 31378 12 22 0.999701 0.999402 0.308866 0.999551 2.296566 1.861933 1.883951 2.123073 ``` Notice that F1 scores are above 0.999 for SNPs and above 0.995 for indels! diff --git a/docs/deepvariant-ont-r104-duplex-case-study.md b/docs/deepvariant-ont-r104-duplex-case-study.md index bc2c5971..372178fb 100644 --- a/docs/deepvariant-ont-r104-duplex-case-study.md +++ b/docs/deepvariant-ont-r104-duplex-case-study.md @@ -75,7 +75,7 @@ mkdir -p "${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}":"${INPUT_DIR}" \ @@ -153,10 +153,10 @@ Output: ``` Benchmarking Summary: Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio -INDEL ALL 11256 10306 950 20226 709 8823 343 276 0.915601 0.937823 0.436221 0.926579 NaN NaN 1.561710 2.045850 -INDEL PASS 11256 10306 950 20226 709 8823 343 276 0.915601 0.937823 0.436221 0.926579 NaN NaN 1.561710 2.045850 - SNP ALL 71333 71274 59 96103 69 24718 36 23 0.999173 0.999033 0.257203 0.999103 2.314904 1.927434 1.715978 1.647902 - SNP PASS 71333 71274 59 96103 69 24718 36 23 0.999173 0.999033 0.257203 0.999103 2.314904 1.927434 1.715978 1.647902 +INDEL ALL 11256 10372 884 21138 697 9801 364 214 0.921464 0.938520 0.463667 0.929914 NaN NaN 1.561710 2.008049 +INDEL PASS 11256 10372 884 21138 697 9801 364 214 0.921464 0.938520 0.463667 0.929914 NaN NaN 1.561710 2.008049 + SNP ALL 71333 71304 29 110055 63 38637 19 22 0.999593 0.999118 0.351070 0.999356 2.314904 1.752724 1.715978 1.562169 + SNP PASS 71333 71304 29 110055 63 38637 19 22 0.999593 0.999118 0.351070 0.999356 2.314904 1.752724 1.715978 1.562169 ``` ## Acknowledgement diff --git a/docs/deepvariant-ont-r104-simplex-case-study.md b/docs/deepvariant-ont-r104-simplex-case-study.md index 97edd76e..7f0a2b09 100644 --- a/docs/deepvariant-ont-r104-simplex-case-study.md +++ b/docs/deepvariant-ont-r104-simplex-case-study.md @@ -74,7 +74,7 @@ mkdir -p "${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}" \ @@ -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