Update all case studies for v1.6.1 release

kishwarshafin · kishwarshafin · commit f575751cd629 · 2024-03-18T19:31:52.000Z
PiperOrigin-RevId: 616265600
diff --git a/.github/ISSUE_TEMPLATE/problem_report.md b/.github/ISSUE_TEMPLATE/problem_report.md
@@ -7,7 +7,7 @@ assignees: ''
 
 ---
 
-**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6/docs/FAQ.md**:
+**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**:
 
 **Describe the issue:**
 (A clear and concise description of what the issue is.)
diff --git a/.github/ISSUE_TEMPLATE/question.md b/.github/ISSUE_TEMPLATE/question.md
@@ -7,6 +7,6 @@ assignees: ''
 
 ---
 
-**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6/docs/FAQ.md**:
+**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**:
 
 
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <img src="docs/images/dv_logo.png" width=50% height=50%>
 
-[![release](https://img.shields.io/badge/release-v1.6.0-green?logo=github)](https://github.com/google/deepvariant/releases)
+[![release](https://img.shields.io/badge/release-v1.6.1-green?logo=github)](https://github.com/google/deepvariant/releases)
 [![announcements](https://img.shields.io/badge/announcements-blue)](https://groups.google.com/d/forum/deepvariant-announcements)
 [![blog](https://img.shields.io/badge/blog-orange)](https://goo.gl/deepvariant)
 
@@ -70,7 +70,7 @@ Please also note:
 We recommend using our Docker solution. The command will look like this:
 
 ```
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 docker run \
   -v "YOUR_INPUT_DIR":"/input" \
   -v "YOUR_OUTPUT_DIR:/output" \
diff --git a/docs/FAQ.md b/docs/FAQ.md
@@ -143,7 +143,7 @@ container, you can `ls` inside the container. For example, using the setup shown
 in the README and looking inside the `/input` volume:
 
 ```
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 docker run \
   -v "YOUR_INPUT_DIR":"/input" \
   -v "YOUR_OUTPUT_DIR:/output" \
@@ -158,7 +158,7 @@ and outside the Docker container.
 ```
 echo $HOME # see what your home directory is first.
 ls $HOME
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 sudo docker run \
   -v "${HOME}":"${HOME}" \
   google/deepvariant:"${BIN_VERSION}" \
@@ -171,7 +171,7 @@ Since the DeepVariant v0.9 release, we recommend
 "[Best practices for multi-sample variant calling with DeepVariant](https://github.com/google/deepvariant/blob/r0.9/docs/trio-merge-case-study.md)".
 
 For specifically calling on duos or trios, we introduced
-[DeepTrio](https://github.com/google/deepvariant/blob/r1.6/docs/deeptrio-details.md)
+[DeepTrio](https://github.com/google/deepvariant/blob/r1.6.1/docs/deeptrio-details.md)
 in v1.1.
 
 ## Why am I seeing "CUDA_ERROR_NOT_INITIALIZED: initialization error" while running on GPU?
diff --git a/docs/deeptrio-pacbio-case-study.md b/docs/deeptrio-pacbio-case-study.md
@@ -85,7 +85,7 @@ is run as a separate command.
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo apt -y update
 sudo apt-get -y install docker.io
diff --git a/docs/deeptrio-quick-start.md b/docs/deeptrio-quick-start.md
@@ -32,7 +32,7 @@ documentation on how to build.
 ### Get Docker image
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo apt -y update
 sudo apt-get -y install docker.io
@@ -341,7 +341,7 @@ INDEL   PASS            2         2         0            2         0          0
 [BAM]: http://genome.sph.umich.edu/wiki/BAM
 [BWA]: https://academic.oup.com/bioinformatics/article/25/14/1754/225615/Fast-and-accurate-short-read-alignment-with
 [docker build]: https://docs.docker.com/engine/reference/commandline/build/
-[Dockerfile]: https://github.com/google/deepvariant/blob/r1.6/Dockerfile.deeptrio
+[Dockerfile]: https://github.com/google/deepvariant/blob/r1.6.1/Dockerfile.deeptrio
 [FASTA]: https://en.wikipedia.org/wiki/FASTA_format
 [VCF]: https://samtools.github.io/hts-specs/VCFv4.3.pdf
 [run_deeptrio.py]: ../scripts/run_deeptrio.py
diff --git a/docs/deeptrio-wgs-case-study.md b/docs/deeptrio-wgs-case-study.md
@@ -82,7 +82,7 @@ command.
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker pull google/deepvariant:deeptrio-"${BIN_VERSION}"
 
diff --git a/docs/deepvariant-case-study.md b/docs/deepvariant-case-study.md
@@ -67,7 +67,7 @@ DeepVariant pipeline consists of 3 steps: `make_examples`, `call_variants`, and
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${PWD}/input":"/input" \
diff --git a/docs/deepvariant-complete-g400-case-study.md b/docs/deepvariant-complete-g400-case-study.md
@@ -52,7 +52,7 @@ On a CPU-only machine:
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="1.6.0rc4"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${PWD}/input":"/input" \
diff --git a/docs/deepvariant-complete-t7-case-study.md b/docs/deepvariant-complete-t7-case-study.md
@@ -52,7 +52,7 @@ On a CPU-only machine:
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${PWD}/input":"/input" \
diff --git a/docs/deepvariant-exome-case-study.md b/docs/deepvariant-exome-case-study.md
@@ -68,7 +68,7 @@ curl ${HTTPDIR}/idt_capture_novogene.grch38.bed > input/idt_capture_novogene.grc
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${PWD}/input":"/input" \
diff --git 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="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${PWD}/input":"/input" \
diff --git a/docs/deepvariant-ont-r104-duplex-case-study.md b/docs/deepvariant-ont-r104-duplex-case-study.md
@@ -75,7 +75,7 @@ mkdir -p "${OUTPUT_DIR}/${INTERMEDIATE_DIRECTORY}"
 We will run DeepVariant from docker using the `run_deepvariant` script.
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${INPUT_DIR}":"${INPUT_DIR}" \
diff --git 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="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker run \
   -v "${INPUT_DIR}":"${INPUT_DIR}" \
diff --git a/docs/deepvariant-pacbio-model-case-study.md b/docs/deepvariant-pacbio-model-case-study.md
@@ -79,7 +79,7 @@ curl ${HTTPDIR}/HG003.GRCh38.chr20.pFDA_truthv2.bam.bai > input/HG003.GRCh38.chr
 
 ```bash
 ulimit -u 10000 # https://stackoverflow.com/questions/52026652/openblas-blas-thread-init-pthread-create-resource-temporarily-unavailable/54746150#54746150
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 mkdir -p deepvariant_output
 
 singularity exec --bind /usr/lib/locale/ \
diff --git a/docs/deepvariant-quick-start.md b/docs/deepvariant-quick-start.md
@@ -33,7 +33,7 @@ If you want to compile the DeepVariant binaries for yourself, we also have a
 ### Get Docker image
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo apt -y update
 sudo apt-get -y install docker.io
@@ -254,7 +254,7 @@ INDEL   PASS            4         4         0           13         0          9
 [BAM]: http://genome.sph.umich.edu/wiki/BAM
 [BWA]: https://academic.oup.com/bioinformatics/article/25/14/1754/225615/Fast-and-accurate-short-read-alignment-with
 [docker build]: https://docs.docker.com/engine/reference/commandline/build/
-[Dockerfile]: https://github.com/google/deepvariant/blob/r1.6/Dockerfile
+[Dockerfile]: https://github.com/google/deepvariant/blob/r1.6.1/Dockerfile
 [FASTA]: https://en.wikipedia.org/wiki/FASTA_format
 [Quick Start in r0.7]: https://github.com/google/deepvariant/blob/r0.7/docs/deepvariant-quick-start.md
 [VCF]: https://samtools.github.io/hts-specs/VCFv4.3.pdf
diff --git a/docs/deepvariant-training-case-study.md b/docs/deepvariant-training-case-study.md
@@ -62,7 +62,7 @@ YOUR_PROJECT=REPLACE_WITH_YOUR_PROJECT
 OUTPUT_GCS_BUCKET=REPLACE_WITH_YOUR_GCS_BUCKET
 
 BUCKET="gs://deepvariant"
-VERSION="1.6.0"
+VERSION="1.6.1"
 DOCKER_IMAGE="google/deepvariant:${VERSION}"
 
 MODEL_BUCKET="${BUCKET}/models/DeepVariant/${VERSION}/DeepVariant-inception_v3-${VERSION}+data-wgs_standard"
@@ -115,7 +115,7 @@ gsutil -m cp -r "${DATA_BUCKET}/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Io
 ```bash
 sudo apt -y update
 sudo apt -y install parallel
-curl -O https://raw.githubusercontent.com/google/deepvariant/r1.6/scripts/install_nvidia_docker.sh
+curl -O https://raw.githubusercontent.com/google/deepvariant/r1.6.1/scripts/install_nvidia_docker.sh
 bash -x install_nvidia_docker.sh
 ```
 
@@ -187,7 +187,7 @@ cat "${OUTPUT_DIR}/training_set.with_label.tfrecord-00000-of-00016.gz.example_in
 
 ```json
 {
-  "version": "1.6.0",
+  "version": "1.6.1",
   "shape": [100, 221, 7],
   "channels": [1, 2, 3, 4, 5, 6, 19]
 }
@@ -280,7 +280,7 @@ Then, get the script that performs shuffling:
 
 ```bash
 mkdir -p ${SHUFFLE_SCRIPT_DIR}
-wget https://raw.githubusercontent.com/google/deepvariant/r1.6/tools/shuffle_tfrecords_beam.py -O ${SHUFFLE_SCRIPT_DIR}/shuffle_tfrecords_beam.py
+wget https://raw.githubusercontent.com/google/deepvariant/r1.6.1/tools/shuffle_tfrecords_beam.py -O ${SHUFFLE_SCRIPT_DIR}/shuffle_tfrecords_beam.py
 ```
 
 Next, we shuffle the data using DataflowRunner. Before that, please make sure
@@ -389,7 +389,7 @@ training parameters. Parameters within this training file can be overridden when
 we run `train` by passing `--config.<param>=<value>`.
 
 ```bash
-curl https://raw.githubusercontent.com/google/deepvariant/r1.6/deepvariant/dv_config.py > dv_config.py
+curl https://raw.githubusercontent.com/google/deepvariant/r1.6.1/deepvariant/dv_config.py > dv_config.py
 ```
 
 ### Start `train`
@@ -406,7 +406,7 @@ this dataset, and are not recommended as the best default either.
     --config=dv_config.py:base \
     --config.train_dataset_pbtxt="${OUTPUT_BUCKET}/training_set.dataset_config.pbtxt" \
     --config.tune_dataset_pbtxt="${OUTPUT_DIR}/validation_set.dataset_config.pbtxt" \
-    --config.init_checkpoint=gs://deepvariant/models/DeepVariant/1.6.0/checkpoints/wgs/deepvariant.wgs.ckpt \
+    --config.init_checkpoint=gs://deepvariant/models/DeepVariant/1.6.1/checkpoints/wgs/deepvariant.wgs.ckpt \
     --config.num_epochs=10 \
     --config.learning_rate=0.0001 \
     --config.num_validation_examples=0 \
diff --git a/docs/deepvariant-vg-case-study.md b/docs/deepvariant-vg-case-study.md
@@ -181,7 +181,7 @@ And then, run DeepVariant.
 [DeepVariant Case Study](deepvariant-case-study.md).)
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker pull google/deepvariant:"${BIN_VERSION}"
 
@@ -253,7 +253,7 @@ INDEL   PASS       504501    502199      2302       960061      1526     434935
 | SNP   | 3316515  | 10981    | 5550     | 0.9967        | 0.99833          | 0.997514        |
 
 This can be compared with
-https://github.com/google/deepvariant/blob/r1.6/docs/metrics.md#accuracy.
+https://github.com/google/deepvariant/blob/r1.6.1/docs/metrics.md#accuracy.
 
 Which shows that `vg giraffe` improves F1:
 
diff --git a/docs/deepvariant-xy-calling-case-study.md b/docs/deepvariant-xy-calling-case-study.md
@@ -72,7 +72,7 @@ mkdir -p "${OUTPUT_DIR}/${INTERMEDIATE_DIRECTORY}"
 We will run DeepVariant from docker using the `run_deepvariant` script.
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker pull google/deepvariant:"${BIN_VERSION}"
 
diff --git a/docs/runtime-by-region.md b/docs/runtime-by-region.md
@@ -47,7 +47,7 @@ make_examples runtime by region data. Continuing from the quick start, it looks
 like this:
 
 ```bash
-BIN_VERSION="1.6.0" # Only available in v1.1+.
+BIN_VERSION="1.6.1" # Only available in v1.1+.
 docker run \
   -v "INPUT_DIR":"/input" \
   -v "OUTPUT_DIR:/output" \
diff --git a/docs/show-examples.md b/docs/show-examples.md
@@ -48,7 +48,7 @@ Once you have a make_examples output tfrecord file, then you can run
 INPUT_DIR="${PWD}/quickstart-testdata"
 OUTPUT_DIR="${PWD}/quickstart-output"
 
-BIN_VERSION="1.6.0"  # show_examples is available only in version 1.0.0 and later.
+BIN_VERSION="1.6.1"  # show_examples is available only in version 1.0.0 and later.
 sudo docker run \
   -v "${INPUT_DIR}":"/input" \
   -v "${OUTPUT_DIR}":"/output" \
diff --git a/docs/trio-merge-case-study.md b/docs/trio-merge-case-study.md
@@ -115,7 +115,7 @@ serially is not the most effective approach.
 ```
 N_SHARDS=$(nproc)  # Or change to the number of cores you want to use
 CAPTURE_BED=agilent_sureselect_human_all_exon_v5_b37_targets.bed
-VERSION=1.6.0
+VERSION=1.6.1
 
 declare -a trio=(HG002 HG003 HG004)
 for SAMPLE in "${trio[@]}"

Original file line number	Diff line number	Diff line change
`@@ -7,6 +7,6 @@ assignees: ''`
`7`	`7`
`8`	`8`	`---`
`9`	`9`
`10`		`-Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6/docs/FAQ.md:`
	`10`	`+Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md:`
`11`	`11`
`12`	`12`