doc updates for release

kishwarshafin · Nov 2, 2021 · da61114 · da61114
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diff --git a/README.md b/README.md
@@ -8,13 +8,12 @@
 </p>
 
 ---
-### Version 0.5 update
+### Version 0.6 update
 
-We have updated PEPPER to support `Guppy v5.0.7`. The current v0.5 only supports ONT variant calling.
-
-**NOTE: The models of v0.5 are trained with Guppy v5.0.7 "sup" mode. If you use have Guppy v4.X data, [please use PEPPER v0.4](https://github.com/kishwarshafin/pepper/tree/r0.4)**
-
-**If you want to use PEPPER-Margin-DeepVariant for assembly polishing or PacBio HiFi variant calling, [please use PEPPER v0.4](https://github.com/kishwarshafin/pepper/tree/r0.4)**
+PEPPER-Margin-deepvariant v0.6 supports:
+* Oxford Nanopore Variant calling for Guppy 5.0.7 "Sup" basecaller
+* Oxford Nanopore Variant calling for R10.4 Q20
+* PacBio-HiFi data
 
 ---
 
@@ -23,24 +22,33 @@ Please cite the following manuscript if you are using `PEPPER-Margin-DeepVariant
 
 
 <details>
-<summary><a href="https://www.biorxiv.org/content/10.1101/2021.03.04.433952v1"><b>bioRxiv:</b> Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks.</a></summary>
+<summary><a href="https://www.nature.com/articles/s41592-021-01299-w"><b>Nature Methods:</b> Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks.</a></summary>
 Authors: Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, <br/> Gunjan Baid, Jordan M Eizenga, Karen H Miga, Paolo Carnevali, Miten Jain, Andrew Carroll, Benedict Paten.
 </details>
 
 ---
 ### Quickstart
 Please follow the quickstart guides to assess your setup. Please follow case-study documentations for detailed instructions.
+#### Oxford Nanopore
+* **Docker**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_docker_quickstart.md).
+* **Singularity**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_singularity_quickstart.md).
+
+#### PacBio-HiFi
 * **Docker**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_docker_quickstart.md).
 * **Singularity**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_singularity_quickstart.md).
 
 ### Case studies
 
 The variant calling pipeline can be run on [Docker](https://docs.docker.com/install/linux/docker-ce/ubuntu/) or [Singularity](https://sylabs.io/guides/3.7/user-guide/quick_start.html#quick-installation-steps). The case studies are designed on `chr20` of `HG002` sample.
 
+#### Oxford Nanopore Variant calling
 The case-studies include input data and benchmarking of the run:
 * Nanopore variant calling using **Docker**: [Link](./docs/pipeline_docker/ONT_variant_calling.md)
 * Nanopore variant calling using **Singularity**: [Link](./docs/pipeline_singularity/ONT_variant_calling_singularity.md)
-* Nanopore variant calling using **NVIDIA-docker**: [Link](./docs/pipeline_docker_gpu/ONT_variant_calling_gpu.md)
+
+#### PacBio-HiFi variant calling
+* Nanopore variant calling using **Docker**: [Link](./docs/pipeline_docker/ONT_variant_calling.md)
+* Nanopore variant calling using **Singularity**: [Link](./docs/pipeline_singularity/ONT_variant_calling_singularity.md)
 
 ### License
 [PEPPER license](./LICENSE), [Margin License](https://github.com/UCSC-nanopore-cgl/margin/blob/master/LICENSE.txt) and [DeepVariant License](https://github.com/google/deepvariant/blob/r1.1/LICENSE) extend to the trained models (PEPPER, Margin and DeepVariant) and container environment (Docker and Singularity).
@@ -57,7 +65,7 @@ We are thankful to the developers of these packages:
 
 
 ### Fun Fact
-<img src="https://vignette.wikia.nocookie.net/marveldatabase/images/7/72/Anthony_Stark_%28Earth-616%29_from_Iron_Man_Vol_5_2_002.jpg/revision/latest?cb=20130407031815" alt="guppy235" width="240p"> <br/>
+<img src="https://vignette.wikia.nocookie.net/marveldatabase/images/7/72/Anthony_Stark_%28Earth-616%29_from_Iron_Man_Vol_5_2_002.jpg/revision/latest?cb=20130407031815" alt="Iron-Man" width="240p"> <br/>
 
 The name "P.E.P.P.E.R." is inspired from an A.I. created by Tony Stark in the  Marvel Comics (Earth-616).
 

diff --git a/docs/pipeline_docker/HiFi_variant_calling.md b/docs/pipeline_docker/HiFi_variant_calling.md
@@ -1,13 +1,13 @@
 ## PacBio HiFi variant calling workflow
 PEPPER-Margin-DeepVariant is a haplotype-aware variant calling pipeline for long reads.
 
-<img src="../../img/PMDV_variant_calling_HiFi.png" alt="PEPPER-Margin-DeepVariant Variant Calling Workflow">
+<img src="../../img/PMDV_variant_calling_HiFi_v6.png" alt="PEPPER-Margin-DeepVariant Variant Calling Workflow">
 
 ----
-### PacBio HiFi HG002 chr20 case-study
+### PacBio HiFi HG003 chr20 case-study
 We evaluated this pipeline on `~35x` HG002 data. The data is publicly available, please feel free to download, run and evaluate the pipeline.
 ```bash
-Sample:     HG002
+Sample:     HG003
 Coverage:   ~35x
 Region:     chr20
 Reference:  GRCh38_no_alt
@@ -62,7 +62,8 @@ BASE="${HOME}/hifi-case-study"
 # Set up input data
 INPUT_DIR="${BASE}/input/data"
 REF="GRCh38_no_alt.chr20.fa"
-BAM="HG002_PacBio_HiFi_35x_2_GRCh38_no_alt.chr20.bam"
+BAM="HG003.GRCh38.chr20.pFDA_truthv2.bam"
+OUTPUT_VCF="PEPPER_MARGIN_DEEPVARIANT_OUTPUT.vcf.gz"
 
 # Set the number of CPUs to use
 THREADS="64"
@@ -73,83 +74,45 @@ OUTPUT_DIR="${BASE}/output"
 ## Create local directory structure
 mkdir -p "${OUTPUT_DIR}"
 mkdir -p "${INPUT_DIR}"
+mkdir -p input
 
 # Download the data to input directory
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_PacBio_HiFi_35x_2_GRCh38_no_alt.chr20.bam
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_PacBio_HiFi_35x_2_GRCh38_no_alt.chr20.bam.bai
+wget -P ${INPUT_DIR} https://downloads.pacbcloud.com/public/dataset/HG003/deepvariant-case-study/HG003.GRCh38.chr20.pFDA_truthv2.bam
+wget -P ${INPUT_DIR} https://downloads.pacbcloud.com/public/dataset/HG003/deepvariant-case-study/HG003.GRCh38.chr20.pFDA_truthv2.bam.bai
 wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/GRCh38_no_alt.chr20.fa
 wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/GRCh38_no_alt.chr20.fa.fai
 ```
 
 ##### Step 3: Run PEPPER-Margin to generate a phased bam
 ```bash
 ## Pull the docker image.
-sudo docker pull kishwars/pepper_deepvariant:r0.4
+sudo docker pull kishwars/pepper_deepvariant:r0.6
 
 # Run PEPPER-Margin-DeepVariant
 sudo docker run --ipc=host \
 -v "${INPUT_DIR}":"${INPUT_DIR}" \
 -v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
-kishwars/pepper_deepvariant:r0.4 \
+kishwars/pepper_deepvariant:r0.6 \
 run_pepper_margin_deepvariant call_variant \
 -b "${INPUT_DIR}/${BAM}" \
 -f "${INPUT_DIR}/${REF}" \
 -o "${OUTPUT_DIR}" \
--t ${THREADS} \
---ccs
-
-# This generates a Phased bam in the output directory: MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam
-```
-##### Step 4: Run DeepVariant
-```bash
-PHASED_BAM=MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam
-OUTPUT_PREFIX="HG002_HiFi_35x_2_GRCh38_PEPPER_Margin_DeepVariant.chr20"
-OUTPUT_VCF="HG002_HiFi_35x_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz"
-
-sudo docker pull google/deepvariant:1.1.0
-
-sudo docker run \
--v "${INPUT_DIR}":"${INPUT_DIR}" \
--v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
-google/deepvariant:1.1.0 \
-/opt/deepvariant/bin/run_deepvariant \
---model_type=PACBIO \
---ref="${INPUT_DIR}/${REF}" \
---reads="${OUTPUT_DIR}/${PHASED_BAM}" \
---output_vcf="${OUTPUT_DIR}/${OUTPUT_VCF}" \
---num_shards=${THREADS} \
---use_hp_information
-```
-
-##### Step 5: Phase the output VCF with Margin (Optional)
-```bash
-sudo docker run --ipc=host \
--v "${INPUT_DIR}":"${INPUT_DIR}" \
--v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
-kishwars/pepper_deepvariant:r0.4 \
-margin phase \
-"${INPUT_DIR}/${BAM}" \
-"${INPUT_DIR}/${REF}" \
-"${OUTPUT_DIR}/${OUTPUT_VCF}" \
-/opt/margin_dir/params/misc/allParams.phase_vcf.json \
--t ${THREADS} \
--M \
--o "${OUTPUT_DIR}/${OUTPUT_PREFIX}"
-
-OUTPUT_PHASED_VCF=${OUTPUT_PREFIX}.phased.vcf
+-t "${THREADS}" \
+--hifi
 ```
 
 ###### Evaluation using hap.py (Optional)
 You can evaluate the variants using `hap.py`.
 Download benchmarking data:
 ```bash
 # Set up input data
-TRUTH_VCF="HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
-TRUTH_BED="HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
+TRUTH_VCF="HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
+TRUTH_BED="HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
 
 # Download truth VCFs
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
+wget -P ${INPUT_DIR} ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
+wget -P ${INPUT_DIR} ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
+wget -P ${INPUT_DIR} ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
 ```
 
 Run hap.py:
@@ -177,8 +140,8 @@ ${OUTPUT_DIR}/${OUTPUT_VCF} \
 
 |  Type | Truth<br>total | True<br>positives | False<br>negatives | False<br>positives |  Recall  | Precision | F1-Score |
 |:-----:|:--------------:|:-----------------:|:------------------:|:------------------:|:--------:|:---------:|:--------:|
-| INDEL |      11256     |       11175       |         81         |         94         | 0.992804 |  0.991953 | 0.992378 |
-|  SNP  |      71333     |       71277       |         56         |          8         | 0.999215 |  0.999888 | 0.999551 |
+| INDEL |      10628     |       10562       |         66         |         60         | 0.993790 |  0.994577 | 0.994183 |
+|  SNP  |      70166     |       70140       |         26         |         17         | 0.999629 |  0.999758 | 0.999694 |
 
 ### Authors:
 This pipeline is developed in a collaboration between UCSC genomics institute and the genomics team at Google health.
diff --git a/docs/pipeline_docker/ONT_variant_calling.md b/docs/pipeline_docker/ONT_variant_calling.md
@@ -10,7 +10,7 @@ We evaluated this pipeline on `~30x` HG002 data. The data is publicly available,
 ```bash
 Sample:     HG002
 Coverage:   ~25-90x
-Basecaller: Guppy 5.0.7 or higher
+Basecaller: Guppy 5.0.7 "SUP"
 Region:     chr20
 Reference:  GRCh38_no_alt
 ```
@@ -72,7 +72,7 @@ THREADS="64"
 # Set up output directory
 OUTPUT_DIR="${BASE}/output"
 OUTPUT_PREFIX="HG002_ONT_30x_2_GRCh38_PEPPER_Margin_DeepVariant.chr20"
-OUTPUT_VCF="HG002_ONT_30x_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz"
+OUTPUT_VCF="PEPPER_MARGIN_DEEPVARIANT_OUTPUT.vcf.gz"
 
 ## Create local directory structure
 mkdir -p "${OUTPUT_DIR}"
@@ -88,25 +88,19 @@ wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/us
 ##### Step 3: Run PEPPER-Margin-DeepVariant
 ```bash
 ## Pull the docker image.
-sudo docker pull kishwars/pepper_deepvariant:r0.5
+sudo docker pull kishwars/pepper_deepvariant:r0.6
 
 # Run PEPPER-Margin-DeepVariant
-sudo docker run --ipc=host \
+sudo docker run \
 -v "${INPUT_DIR}":"${INPUT_DIR}" \
 -v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
-kishwars/pepper_deepvariant:r0.5 \
+kishwars/pepper_deepvariant:r0.6 \
 run_pepper_margin_deepvariant call_variant \
 -b "${INPUT_DIR}/${BAM}" \
 -f "${INPUT_DIR}/${REF}" \
 -o "${OUTPUT_DIR}" \
--p "${OUTPUT_PREFIX}" \
--t ${THREADS} \
---ont
-
-# Optional parameters:
-# -s HG002 # optional: Sets Sample Name
-# --gvcf # optional: Produces gVCF output
-# --phased_output # optional: Produces phased output
+-t "${THREADS}" \
+--ont_r9_guppy5_sup # For R10.4 Q20 reads set: --ont_r10_q20
 ```
 
 ###### Evaluation using hap.py (Optional)
@@ -148,8 +142,8 @@ ${OUTPUT_DIR}/${OUTPUT_VCF} \
 
 |  Type | Truth<br>total | True<br>positives | False<br>negatives | False<br>positives |  Recall  | Precision | F1-Score |
 |:-----:|:--------------:|:-----------------:|:------------------:|:------------------:|:--------:|:---------:|:--------:|
-| INDEL |      11256     |        7136       |        4120        |        2137        | 0.633973 |  0.771688 | 0.696084 |
-|  SNP  |      71333     |       71004       |         329        |         322        | 0.995388 |  0.995487 | 0.995437 |
+| INDEL |      11256     |        6897       |        4359        |        1211        | 0.61274  |  0.853443 | 0.713333 |
+|  SNP  |      71333     |       71012       |         321        |         256        | 0.99550  |  0.996409 | 0.995954 |
 
 ### Authors:
 This pipeline is developed in a collaboration between UCSC genomics institute and the genomics team at Google health.
diff --git a/docs/pipeline_singularity/HiFi_variant_calling_singularity.md b/docs/pipeline_singularity/HiFi_variant_calling_singularity.md
@@ -1,13 +1,13 @@
 ## PacBio HiFi variant calling workflow [Using singularity]
 PEPPER-Margin-DeepVariant is a haplotype-aware variant calling pipeline for long reads.
 
-<img src="../../img/PMDV_variant_calling_HiFi.png" alt="PEPPER-Margin-DeepVariant Variant Calling Workflow">
+<img src="../../img/PMDV_variant_calling_HiFi_v6.png" alt="PEPPER-Margin-DeepVariant Variant Calling Workflow">
 
 ----
 ### PacBio HiFi HG002 chr20 case-study
 We evaluated this pipeline on `~35x` HG002 data.
 ```bash
-Sample:     HG002
+Sample:     HG003
 Coverage:   ~35x
 Region:     chr20
 Reference:  GRCh38_no_alt
@@ -64,7 +64,8 @@ BASE="${HOME}/hifi-case-study"
 # Set up input data
 INPUT_DIR="${BASE}/input/data"
 REF="GRCh38_no_alt.chr20.fa"
-BAM="HG002_PacBio_HiFi_35x_2_GRCh38_no_alt.chr20.bam"
+BAM="HG003.GRCh38.chr20.pFDA_truthv2.bam"
+OUTPUT_VCF="PEPPER_MARGIN_DEEPVARIANT_OUTPUT.vcf.gz"
 
 # Set the number of CPUs to use
 THREADS="64"
@@ -75,81 +76,43 @@ OUTPUT_DIR="${BASE}/output"
 ## Create local directory structure
 mkdir -p "${OUTPUT_DIR}"
 mkdir -p "${INPUT_DIR}"
+mkdir -p input
 
 # Download the data to input directory
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_PacBio_HiFi_35x_2_GRCh38_no_alt.chr20.bam
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_PacBio_HiFi_35x_2_GRCh38_no_alt.chr20.bam.bai
+wget -P ${INPUT_DIR} https://downloads.pacbcloud.com/public/dataset/HG003/deepvariant-case-study/HG003.GRCh38.chr20.pFDA_truthv2.bam
+wget -P ${INPUT_DIR} https://downloads.pacbcloud.com/public/dataset/HG003/deepvariant-case-study/HG003.GRCh38.chr20.pFDA_truthv2.bam.bai
 wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/GRCh38_no_alt.chr20.fa
 wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/GRCh38_no_alt.chr20.fa.fai
 ```
 
 ##### Step 3: Run PEPPER-Margin to generate a phased bam
 ```bash
 ## Pull the docker image to sigularity, this is a 6.6GB download
-singularity pull docker://kishwars/pepper_deepvariant:r0.4
-
-# The pull command creates pepper_deepvariant_r0.4.sif file locally
+singularity pull docker://kishwars/pepper_deepvariant:r0.6
 
 # Run PEPPER-Margin-DeepVariant
 singularity exec --bind /usr/lib/locale/ \
-pepper_deepvariant_r0.4.sif \
+pepper_deepvariant_r0.6.sif \
 run_pepper_margin_deepvariant call_variant \
 -b "${INPUT_DIR}/${BAM}" \
 -f "${INPUT_DIR}/${REF}" \
 -o "${OUTPUT_DIR}" \
 -t ${THREADS} \
---ccs
-
-# This generates a Phased bam in the output directory: MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam
-```
-##### Step 4: Run DeepVariant
-```bash
-PHASED_BAM=MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam
-OUTPUT_PREFIX="HG002_HiFi_35x_2_GRCh38_PEPPER_Margin_DeepVariant.chr20"
-OUTPUT_VCF="HG002_HiFi_35x_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz"
-
-singularity pull docker://google/deepvariant:1.1.0
-
-# The pull command creates deepvariant_1.1.0.sif file locally
-
-singularity exec --bind /usr/lib/locale/ \
-deepvariant_1.1.0.sif \
-/opt/deepvariant/bin/run_deepvariant \
---model_type=PACBIO \
---ref="${INPUT_DIR}/${REF}" \
---reads="${OUTPUT_DIR}/${PHASED_BAM}" \
---output_vcf="${OUTPUT_DIR}/${OUTPUT_VCF}" \
---num_shards=${THREADS} \
---use_hp_information
-```
-
-##### Step 5: Phase the output VCF with Margin (Optional)
-```bash
-singularity exec --bind /usr/lib/locale/ \
-pepper_deepvariant_r0.4.sif \
-margin phase \
-"${INPUT_DIR}/${BAM}" \
-"${INPUT_DIR}/${REF}" \
-"${OUTPUT_DIR}/${OUTPUT_VCF}" \
-/opt/margin_dir/params/misc/allParams.phase_vcf.json \
--t ${THREADS} \
--M \
--o "${OUTPUT_DIR}/${OUTPUT_PREFIX}"
-
-OUTPUT_PHASED_VCF=${OUTPUT_PREFIX}.phased.vcf
+--hifi
 ```
 
 ###### Evaluation using hap.py (Optional)
 You can evaluate the variants using `hap.py`.
 Download benchmarking data:
 ```bash
 # Set up input data
-TRUTH_VCF="HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
-TRUTH_BED="HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
+TRUTH_VCF="HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
+TRUTH_BED="HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
 
 # Download truth VCFs
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
-wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/usecase_data/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
+wget -P ${INPUT_DIR} ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
+wget -P ${INPUT_DIR} ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
+wget -P ${INPUT_DIR} ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
 ```
 
 Run hap.py:
@@ -178,8 +141,8 @@ ${OUTPUT_DIR}/${OUTPUT_VCF} \
 
 |  Type | Truth<br>total | True<br>positives | False<br>negatives | False<br>positives |  Recall  | Precision | F1-Score |
 |:-----:|:--------------:|:-----------------:|:------------------:|:------------------:|:--------:|:---------:|:--------:|
-| INDEL |      11256     |       11175       |         81         |         94         | 0.992804 |  0.991953 | 0.992378 |
-|  SNP  |      71333     |       71277       |         56         |          8         | 0.999215 |  0.999888 | 0.999551 |
+| INDEL |      10628     |       10560       |         68         |         60         | 0.993602 |  0.994576 | 0.994089 |
+|  SNP  |      70166     |       70140       |         26         |         18         | 0.999629 |  0.999744 | 0.999687 |
 
 ### Authors:
 This pipeline is developed in a collaboration between UCSC genomics institute and the genomics team at Google health.