Update SBX case study documentation.

PiperOrigin-RevId: 805084468

Author: kishwarshafin

docs/README.md

@@ -22,7 +22,7 @@
     [Mapped with VG](pangenome-aware-wgs-vg-case-study.md)
 *   Pangenome-aware DeepVariant WES:
     [Mapped with BWA](pangenome-aware-wes-bwa-case-study.md)
-*   [SBX case study](sbx-case-study.md)
+*   [Roche SBX case study](roche-sbx-case-study.md)
 
 ## Visualization and analysis
 

docs/sbx-case-study.md renamed to docs/roche-sbx-case-study.md

@@ -1,4 +1,4 @@
-# SBX case study for SBX-D and SBX-Fast data
+# Roche SBX case study
 
 ## Prepare environment
 
@@ -20,18 +20,18 @@ curl ${FTPDIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz | gunzip > ref
 curl ${FTPDIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai > reference/GRCh38_no_alt_analysis_set.fasta.fai
 ```
 
-### Download T2T v1.1 truth for benchmarking
+### Download GIAB v4.2.1 truth for benchmarking
 
-We will benchmark our variant calls against T2T v1.1 truth for HG002.
+We will benchmark our variant calls against GIAB v4.2.1 truth for HG002.
 
 ```bash
 mkdir -p benchmark
 
 HTTPDIR=https://storage.googleapis.com/deepvariant/case-study-testdata
 
-curl ${HTTPDIR}/GRCh38_HG2-T2TQ100-V1.1_smvar.vcf.gz > benchmark/GRCh38_HG2-T2TQ100-V1.1_smvar.vcf.gz
-curl ${HTTPDIR}/GRCh38_HG2-T2TQ100-V1.1_smvar.vcf.gz.tbi > benchmark/GRCh38_HG2-T2TQ100-V1.1_smvar.vcf.gz.tbi
-curl ${HTTPDIR}/GRCh38_HG2-T2TQ100-V1.1_smvar.benchmark.bed > benchmark/GRCh38_HG2-T2TQ100-V1.1_smvar.benchmark.bed
+curl ${HTTPDIR}/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz > benchmark/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
+curl ${HTTPDIR}/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi > benchmark/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
+curl ${HTTPDIR}/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed > benchmark/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
 ```
 
 ### Download GBZ built for GRCh38
@@ -43,26 +43,26 @@ HTTPDIR=https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/f
 curl ${HTTPDIR}/hprc-v1.1-mc-grch38.gbz > input/hprc-v1.1-mc-grch38.gbz
 ```
 
-### Download HG002 BAM
+### Download HG002 chr20 BAM
 
-Please download a SBX-D (or SBX-Fast) HG002 BAM and put it in your input dir.
+We will use Roche SBX HG002 chr20 BAM for this case-study.
 
 ```bash
-# Download your HG002 BAM
-HG002_BAM=/input/your_HG002.bam  # This will be used in the command later.
+mkdir -p input
+HTTPDIR=https://storage.googleapis.com/deepvariant/roche-sbx-case-study-testdata
+
+curl ${HTTPDIR}/HG002.roche_sbx.chr20.bam > input/HG002.roche_sbx.chr20.bam
+curl ${HTTPDIR}/HG002.roche_sbx.chr20.bam.bai > input/HG002.roche_sbx.chr20.bam.bai
 ```
 
 ### Download the model
 
-In this case study, we're calling variants on HG002 chr20, and we'll evaluate
-with T2T v1.1 truth. We'll use the "leave-out-HG001" model, which we also left
-out all chromosome 20 from training or tuning. Refer to the technical white
-paper for more details on all experiments.
+In this case study, we're calling variants on HG002 chr20.
 
 ```bash
 mkdir -p model
 
-HTTPDIR=https://storage.googleapis.com/brain-genomics-public/research/sbx/2025/models/leave-out-HG001
+HTTPDIR=https://storage.googleapis.com/brain-genomics-public/research/sbx/2025/model/leave-out-HG001
 
 curl ${HTTPDIR}/model.ckpt.data-00000-of-00001 > model/model.ckpt.data-00000-of-00001
 curl ${HTTPDIR}/model.ckpt.index > model/model.ckpt.index
@@ -75,7 +75,7 @@ curl ${HTTPDIR}/example_info.json > model/example_info.json
 mkdir -p output
 mkdir -p output/intermediate_results_dir
 
-BIN_VERSION="pangenome_aware_deepvariant-head784362481"
+BIN_VERSION="pangenome_aware_deepvariant-sbx"
 
 sudo docker run \
   -v "${PWD}/input":"/input" \
@@ -87,7 +87,7 @@ sudo docker run \
   /opt/deepvariant/bin/run_pangenome_aware_deepvariant \
   --model_type WGS \
   --ref /reference/GRCh38_no_alt_analysis_set.fasta \
-  --reads "${HG002_BAM}" \
+  --reads /input/HG002.roche_sbx.chr20.bam \
   --pangenome /input/hprc-v1.1-mc-grch38.gbz \
   --output_vcf /output/HG002.chr20.output.vcf.gz \
   --output_gvcf /output/HG002.chr20.output.g.vcf.gz \
@@ -114,12 +114,25 @@ sudo docker run \
   -v "${PWD}/happy:/happy" \
   jmcdani20/hap.py:v0.3.12 \
   /opt/hap.py/bin/hap.py \
-  /benchmark/GRCh38_HG2-T2TQ100-V1.1_smvar.vcf.gz \
+  /benchmark/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz \
   /output/HG002.chr20.output.vcf.gz \
-  -f /benchmark/GRCh38_HG2-T2TQ100-V1.1_smvar.benchmark.bed \
+  -f /benchmark/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed \
   -r /reference/GRCh38_no_alt_analysis_set.fasta \
   -o /happy/happy.output \
   --engine=vcfeval \
   --pass-only \
   -l chr20
 ```
+
+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     11237        19        22167        22      10474     10     10       0.998312          0.998119        0.472504         0.998215                     NaN                     NaN                   1.561710                   2.089132
+INDEL   PASS        11256     11237        19        22167        22      10474     10     10       0.998312          0.998119        0.472504         0.998215                     NaN                     NaN                   1.561710                   2.089132
+  SNP    ALL        71333     71286        47        91930        41      20553     12      3       0.999341          0.999426        0.223572         0.999383                2.314904                1.943955                   1.715978                   1.640709
+  SNP   PASS        71333     71286        47        91930        41      20553     12      3       0.999341          0.999426        0.223572         0.999383                2.314904                1.943955                   1.715978                   1.640709
+```
+
+For all Roche SBX 30x BAMs and VCFs follow this [link](https://console.cloud.google.com/storage/browser/brain-genomics-public/research/sbx/2025/).