Update DeepSomatic to 1.6.1

Author: kishwarshafin

README.md

@@ -1,6 +1,6 @@
 # DeepSomatic
 
-[![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)
 

docs/deepsomatic-illumina-case-study.md

@@ -61,7 +61,7 @@ DeepVariant pipeline consists of 3 steps: `make_examples_somatic`, `call_variant
 ### Running on a CPU-only machine
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker pull google/deepsomatic:"${BIN_VERSION}"
 

docs/deepsomatic-pacbio-case-study.md

@@ -19,6 +19,9 @@ and [hap.py](https://github.com/illumina/hap.py),
 
 We will be using GRCh38 for this case study.
 
+The data are originally from
+https://downloads.pacbcloud.com/public/revio/2023Q2/HCC1395/, which has more
+information about the data.
 
 ```bash
 BASE="${HOME}/deepsomatic-pacbio-case-study"
@@ -61,7 +64,7 @@ DeepVariant pipeline consists of 3 steps: `make_examples_somatic`, `call_variant
 ### Running on a CPU-only machine
 
 ```bash
-BIN_VERSION="1.6.0"
+BIN_VERSION="1.6.1"
 
 sudo docker pull google/deepsomatic:"${BIN_VERSION}"
 

docs/deepsomatic-quick-start.md

@@ -24,7 +24,7 @@ Docker image.
 ### 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

docs/metrics.md

@@ -18,10 +18,10 @@ Runtime is  all chromosomes.
 
 Stage                            | Time (wall time)
 -------------------------------- | ------------------
-make_examples_somatic            | 385m39.963s
-call_variants                    | 423m13.271s
-postprocess_variants (with gVCF) | 26m46.040s
-total                            | ~835m = ~13.92h
+make_examples_somatic            | 211m47.27s
+call_variants                    | 255m44.93s
+postprocess_variants (with gVCF) | 27m44.89s
+total                            | ~495m = ~8.25h
 
 ### Accuracy
 
@@ -52,10 +52,10 @@ Runtime is  all chromosomes.
 
 Stage                            | Time (wall time)
 -------------------------------- | ------------------
-make_examples_somatic            | 586m0.088s
-call_variants                    | 409m54.403s
-postprocess_variants (with gVCF) | 46m39.075s
-total                            | ~1043m = ~17.38h
+make_examples_somatic            | 550m49.27s
+call_variants                    | 420m33.01s
+postprocess_variants (with gVCF) | 45m30.93s
+total                            | ~1017m = ~16.95h
 
 ### Accuracy
 
@@ -71,7 +71,7 @@ somp.py results
 ## How to reproduce the metrics on this page
 
 For simplicity and consistency, we report runtime with a
-[CPU instance with 64 CPUs](https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-details.md#command-for-a-cpu-only-machine-on-google-cloud-platform)
+[CPU instance with 64 CPUs](https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-details.md#command-for-a-cpu-only-machine-on-google-cloud-platform)
 This is NOT the fastest or cheapest configuration.
 
 Use `gcloud compute ssh` to log in to the newly created instance.
@@ -80,7 +80,7 @@ Download and run any of the following case study scripts:
 
 ```
 # Get the script.
-curl -O https://raw.githubusercontent.com/google/deepvariant/r1.6/scripts/inference_deepsomatic.sh
+curl -O https://raw.githubusercontent.com/google/deepvariant/r1.6.1/scripts/inference_deepsomatic.sh
 
 # WGS
 bash inference_deepsomatic.sh --model_preset WGS