From 18accae6964c453be115e4ae9ca06e8535f92194 Mon Sep 17 00:00:00 2001 From: pichuan Date: Fri, 23 Mar 2018 17:19:59 -0700 Subject: [PATCH] Update the hap.py evaluation to use --engine=vcfeval and update the accuracy numbers accordingly. PiperOrigin-RevId: 190299321 --- docs/deepvariant-case-study.md | 8 ++++---- docs/deepvariant-exome-case-study.md | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/deepvariant-case-study.md b/docs/deepvariant-case-study.md index 3f4096d8..06341b9c 100644 --- a/docs/deepvariant-case-study.md +++ b/docs/deepvariant-case-study.md @@ -289,13 +289,13 @@ sudo docker run -it \ pkrusche/hap.py /opt/hap.py/bin/hap.py \ "${TRUTH_VCF}" \ "${OUTPUT_VCF}" \ - --preprocess-truth \ -f "${TRUTH_BED}" \ -r "${UNCOMPRESSED_REF}" \ - -o "${OUTPUT_DIR}/happy.output" + -o "${OUTPUT_DIR}/happy.output" \ + --engine=vcfeval ``` Type | # FN | # FP | Recall | Precision | F1\_Score ----- | ---- | ---- | -------- | --------- | --------- -INDEL | 2291 | 918 | 0.995271 | 0.99810 | 0.996684 -SNP | 1909 | 885 | 0.999374 | 0.99971 | 0.999542 +INDEL | 2116 | 1066 | 0.995447 | 0.997794 | 0.996619 +SNP | 1684 | 916 | 0.999447 | 0.999699 | 0.999573 diff --git a/docs/deepvariant-exome-case-study.md b/docs/deepvariant-exome-case-study.md index a80b79c8..5f723890 100644 --- a/docs/deepvariant-exome-case-study.md +++ b/docs/deepvariant-exome-case-study.md @@ -249,19 +249,19 @@ sudo docker run -it \ pkrusche/hap.py /opt/hap.py/bin/hap.py \ "${TRUTH_VCF}" \ "${OUTPUT_VCF}" \ - --preprocess-truth \ -f "${TRUTH_BED}" \ -T "${CAPTURE_BED}" \ -r "${UNCOMPRESSED_REF}" \ - -o "${OUTPUT_DIR}/happy.output" + -o "${OUTPUT_DIR}/happy.output" \ + --engine=vcfeval ``` Here are the results: Type | # FN | # FP | Recall | Precision | F1\_Score ----- | ---- | ---- | -------- | --------- | --------- -INDEL | 150 | 48 | 0.943117 | 0.981080 | 0.961724 -SNP | 46 | 24 | 0.998636 | 0.999288 | 0.998962 +INDEL | 140 | 51 | 0.946154 | 0.979898 | 0.962730 +SNP | 45 | 24 | 0.998666 | 0.999288 | 0.998977 ## Separate models for calling whole genome and exome data