Merge remote-tracking branch 'upstream/main' into remove_hail_docker

# Conflicts: # inputs/values/dockers.json # inputs/values/dockers_azure.json
broadinstitute · Apr 29, 2024 · e1a4dd1 · e1a4dd1
2 parents d779ae8 + 076529c
commit e1a4dd1
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diff --git a/dockerfiles/melt/run_MELT_2.0.5.sh b/dockerfiles/melt/run_MELT_2.0.5.sh
@@ -19,7 +19,7 @@ set -euo pipefail
 ##### Usage statement
 usage(){
 cat <<EOF
-  usage: runMELT.sh bam ref cov read_len mean_is MELT_DIR RUN_DIR REF_VER
+  usage: runMELT.sh bam ref cov read_len mean_is MELT_DIR REF_VER
   Runs MELT for mobile element detection. Requires paired-end deep (>10X) WGS data mapped with BWA.
   Positional arguments (all required):
     bam        Full path to mapped bam file (bam.bai assumed accompanying the BAM)
@@ -28,15 +28,14 @@ cat <<EOF
     read_len   Mean read length of library
     mean_is    Mean insert size of library
     MELT_DIR   Full path to MELT install directory
-    RUN_DIR    Full path to directory for MELT output
     REF_VER    Reference version (19|38)
 EOF
 }
 
 ##### Args parsing and validation
 if [[ "$#" -eq 0 ]]; then
   usage && exit 0;
-elif [[ "$#" -lt 8 ]]; then
+elif [[ "$#" -lt 7 ]]; then
   echo "At least one of the required parameters is not properly set by the given command:"
   temp_args="$@" && echo "$0 ${temp_args}" && exit 1;
 fi
@@ -51,11 +50,10 @@ cov=$3
 read_len=$4
 mean_is=$5
 MELT_DIR=$6
-RUN_DIR=$7
-REF_VER=$8
+REF_VER=$7
 
 ##### Check for required input (unset or empty)
-if [ -z "${bam}" ] || [ -z "${ref}" ] || [ -z "${cov}" ] || [ -z "${read_len}" ] || [ -z "${mean_is}" ] || [ -z "${MELT_DIR}" ] || [ -z "${RUN_DIR}" ] || [ -z "${REF_VER}" ]; then
+if [ -z "${bam}" ] || [ -z "${ref}" ] || [ -z "${cov}" ] || [ -z "${read_len}" ] || [ -z "${mean_is}" ] || [ -z "${MELT_DIR}" ] || [ -z "${REF_VER}" ]; then
   echo "At least one of the required parameters is not properly set by the given command:"
   temp_args="$@" && echo "$0 ${temp_args}" && exit 1; # non-zero exit because it indicates user errror
 fi
@@ -76,20 +74,18 @@ read_len=$( echo "${read_len}" | cut -f1 -d\. )
 mean_is=$( echo "${mean_is}" | cut -f1 -d\. )
 
 ##### remove trailing slash just to make sure
-RUN_DIR="${RUN_DIR%/}"
 MELT_DIR="${MELT_DIR%/}"
 
 ##### Create transposons reference list
 if [[ "$REF_VER" == "38" ]]; then
-  ls "${MELT_DIR}"/me_refs/Hg38/*zip | sed 's/\*//g' > "${RUN_DIR}/transposon_reference.list"
+  ls "${MELT_DIR}"/me_refs/Hg38/*zip | sed 's/\*//g' > "transposon_reference.list"
   GENE_BED_FILE="${MELT_DIR}/add_bed_files/Hg38/Hg38.genes.bed"
 elif [[ "$REF_VER" == "19" ]]; then
-  ls "${MELT_DIR}"/me_refs/1KGP_Hg19/*zip | sed 's/\*//g' > "${RUN_DIR}/transposon_reference.list"
+  ls "${MELT_DIR}"/me_refs/1KGP_Hg19/*zip | sed 's/\*//g' > "transposon_reference.list"
   GENE_BED_FILE="${MELT_DIR}/add_bed_files/1KGP_Hg19/hg19.genes.bed"
 fi
 
-##### Create output directory if it doesn't exist. then run MELT Single
-mkdir -p "${RUN_DIR}" && cd "${RUN_DIR}"
+##### Run MELT Single
 java -Xmx"${JVM_MAX_MEM}" \
   -jar "${MELT_DIR}/MELT.jar" \
   Single \
@@ -99,6 +95,6 @@ java -Xmx"${JVM_MAX_MEM}" \
   -r "${read_len}" \
   -e "${mean_is}" \
   -d "${MIN_CHR_LENGTH}" \
-  -t "${RUN_DIR}/transposon_reference.list" \
+  -t "transposon_reference.list" \
   -n "${GENE_BED_FILE}" \
-  -w "${RUN_DIR}"
+  -w "."
diff --git a/dockerfiles/sv-pipeline-virtual-env/Dockerfile b/dockerfiles/sv-pipeline-virtual-env/Dockerfile
@@ -20,7 +20,7 @@ RUN apt-get -qqy update --fix-missing && \
 # install conda packages
 # NOTE: need to use scipy=1.7.3 instead of scipy=1.8.0 because it makes hail angry
 ARG CONDA_PKGS="cython=0.29.28 numpy=1.22.3 pandas=1.4.2 scipy=1.7.3 scikit-learn=1.0.2 intervaltree=3.1.0 \
-                matplotlib=3.5.1 natsort=8.1.0 google-cloud-dataproc=4.0.2"
+                matplotlib=3.5.1 natsort=8.1.0 google-cloud-dataproc=4.0.2 seaborn=0.12.2"
 RUN mamba install -qy --freeze-installed -n $CONDA_ENV_NAME -c conda-forge -c bioconda $CONDA_PKGS
 
 # copy in HTSLIB install so that pysam uses same version as is available in pipeline
@@ -48,9 +48,9 @@ RUN export SETUPTOOLS_VERSION=$(python -c 'import setuptools; print(setuptools._
     pip install setuptools==$SETUPTOOLS_VERSION
 
 # pybedtools needs to be installed via pip because it doesn't like the updated python
-# hail's latest version is only available via pip or local build
+# hail's latest version is only available via pip or local build. Run cache purge in case the base is out of date.
 ARG PIP_PKGS="pybedtools==0.9.0 hail==0.2.93"
-RUN pip3 --no-cache-dir install $PIP_PKGS
+RUN pip3 cache purge && pip3 --no-cache-dir install $PIP_PKGS
 
 # clean unneeded stuff
 RUN conda clean -ay --force-pkgs-dirs
@@ -79,7 +79,7 @@ RUN export NEW_PACKAGES=$(diff_of_lists.sh "$RUN_DEPS" $APT_REQUIRED_PACKAGES) &
 
 # install R packages
 ARG R_PACKAGES="assertthat beeswarm BH BSDA caret cli crayon DAAG data.table devtools digest dplyr e1071 fansi fpc \
-                generics gert glue HardyWeinberg hash latticeExtra magrittr Matrix metap mnormt nlme nloptr nnet \
+                generics gert glue HardyWeinberg hash latticeExtra magrittr metap mnormt nlme nloptr nnet \
                 numDeriv perm pillar pkgconfig plogr plyr purrr pwr R6 RColorBrewer Rcpp reshape reshape2 rlang ROCR \
                 rpart stringi stringr survival tibble tidyr tidyselect utf8 vioplot withr zoo"
 ARG BIOCONDUCTOR_PKGS="SNPRelate multtest"
@@ -89,6 +89,7 @@ RUN export APT_TRANSIENT_PACKAGES=$(diff_of_lists.sh "$BUILD_DEPS" $APT_REQUIRED
     apt-get -qqy install --no-install-recommends $BUILD_DEPS $(fix_spaces.sh $APT_REQUIRED_PACKAGES) && \
     install_bioconductor_packages.R $BIOCONDUCTOR_PKGS && \
     install_deprecated_R_package.sh "https://cran.r-project.org/src/contrib/Archive/MASS/MASS_7.3-58.tar.gz" && \
+    install_deprecated_R_package.sh "https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz" && \
     install_R_packages.R $R_PACKAGES && \
     apt-get -qqy remove --purge $APT_TRANSIENT_PACKAGES && \
     apt-get -qqy autoremove --purge && \
@@ -100,18 +101,4 @@ RUN export APT_TRANSIENT_PACKAGES=$(diff_of_lists.sh "$BUILD_DEPS" $APT_REQUIRED
            /usr/share/man/?? \
            /usr/share/man/??_*
 
-# Install plink2 & KING (for relatedness inference)
-ARG KING_URL="https://www.kingrelatedness.com/executables/Linux-king215.tar.gz"
-RUN mkdir -p /opt/bin && \
-    cd /opt/bin && \
-    wget -q $KING_URL && \
-    tar -xzf Linux-king215.tar.gz && \
-    rm -f Linux-king215.tar.gz
-
-ARG PLINK2_URL="https://github.com/chrchang/plink-ng/releases/download/2019/plink2_linux_x86_64_20190107.zip"
-RUN cd /opt/bin && \
-    wget -q $PLINK2_URL && \
-    unzip plink2_linux_x86_64_20190107.zip && \
-    rm -f plink2_linux_x86_64_20190107.zip
-
 ENV PATH=/opt/bin:$PATH
diff --git a/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl b/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl
@@ -0,0 +1,38 @@
+{
+  "FilterGenotypes.vcf": {{ test_batch.concordance_vcf | tojson }},
+  "FilterGenotypes.output_prefix": {{ test_batch.name | tojson }},
+  "FilterGenotypes.ploidy_table": {{ test_batch.ploidy_table | tojson }},
+  "FilterGenotypes.truth_json": {{ test_batch.recalibrate_gq_truth_json | tojson }},
+
+  "FilterGenotypes.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
+  "FilterGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
+  "FilterGenotypes.genome_tracks": {{ reference_resources.recalibrate_gq_genome_tracks | tojson }},
+  "FilterGenotypes.recalibrate_gq_args": [
+    "--keep-homvar false",
+    "--keep-homref true",
+    "--keep-multiallelic true",
+    "--skip-genotype-filtering true",
+    "--min-samples-to-estimate-allele-frequency -1"
+  ],
+
+  "FilterGenotypes.ped_file": {{ test_batch.ped_file | tojson }},
+  "FilterGenotypes.site_level_comparison_datasets": [
+    {{ reference_resources.ccdg_abel_site_level_benchmarking_dataset | tojson }},
+    {{ reference_resources.gnomad_v2_collins_site_level_benchmarking_dataset | tojson }},
+    {{ reference_resources.hgsv_byrska_bishop_site_level_benchmarking_dataset | tojson }},
+    {{ reference_resources.thousand_genomes_site_level_benchmarking_dataset | tojson }}
+  ],
+  "FilterGenotypes.sample_level_comparison_datasets": [
+    {{ reference_resources.hgsv_byrska_bishop_sample_level_benchmarking_dataset | tojson }}
+  ],
+  "FilterGenotypes.sample_renaming_tsv": {{ reference_resources.hgsv_byrska_bishop_sample_renaming_tsv | tojson }},
+  "FilterGenotypes.runtime_override_per_sample_benchmark_plot": {
+    "mem_gb": 30,
+    "disk_gb": 50
+  },
+
+  "FilterGenotypes.linux_docker": {{ dockers.linux_docker | tojson }},
+  "FilterGenotypes.gatk_docker": {{ dockers.gq_recalibrator_docker | tojson }},
+  "FilterGenotypes.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
+  "FilterGenotypes.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}
+}
diff --git a/inputs/templates/test/GqRecalibrator/MakeGqRecalibratorTrainingSetFromPacBio.json.tmpl b/inputs/templates/test/GqRecalibrator/MakeGqRecalibratorTrainingSetFromPacBio.json.tmpl
@@ -0,0 +1,19 @@
+{
+  "MakeGqRecalibratorTrainingSetFromPacBio.vcfs": [{{ test_batch.concordance_vcf | tojson }}],
+  "MakeGqRecalibratorTrainingSetFromPacBio.training_sample_ids": {{ test_batch.pacbio_samples_list | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.output_prefix": {{ test_batch.name | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.ploidy_table": {{ test_batch.ploidy_table | tojson }},
+
+"MakeGqRecalibratorTrainingSetFromPacBio.pacbio_sample_ids": {{ test_batch.pacbio_samples | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.vapor_files": {{ test_batch.vapor_files | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.pbsv_vcfs": {{ test_batch.pacbio_pbsv_vcfs | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.pav_vcfs": {{ test_batch.pacbio_pav_vcfs | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.sniffles_vcfs": {{ test_batch.pacbio_sniffles_vcfs | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.reference_dict": {{ reference_resources.reference_dict | tojson }},
+
+  "MakeGqRecalibratorTrainingSetFromPacBio.sv_utils_docker" : {{ dockers.sv_utils_docker | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.gatk_docker" : {{ dockers.gatk_docker | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.sv_base_mini_docker" : {{ dockers.sv_base_mini_docker | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.sv_pipeline_docker" : {{ dockers.sv_pipeline_docker | tojson }},
+  "MakeGqRecalibratorTrainingSetFromPacBio.linux_docker" : {{ dockers.linux_docker | tojson }}
+}
diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -2,20 +2,20 @@
   "name": "dockers",
   "cnmops_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/cnmops:2024-01-24-v0.28.4-beta-9debd6d7",
   "condense_counts_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/gatk:2024-01-15-4.5.0.0-3-gb68fadc5f-NIGHTLY-SNAPSHOT",
+  "gatk_docker": "us.gcr.io/broad-dsde-methods/eph/gatk:2024-02-16-4.5.0.0-8-gcfd4d87ec-NIGHTLY-SNAPSHOT",
   "gatk_docker_pesr_override": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
   "genomes_in_the_cloud_docker": "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "marketplace.gcr.io/google/ubuntu1804",
   "manta_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/manta:2023-09-14-v0.28.3-beta-3f22f94d",
-  "melt_docker": "us.gcr.io/talkowski-sv-gnomad/melt:3159ce1",
+  "melt_docker": "us.gcr.io/talkowski-sv-gnomad/melt:a85c92f",
   "scramble_docker": "us.gcr.io/broad-dsde-methods/markw/scramble:mw-scramble-99af4c50",
   "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
+  "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
+  "sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
+  "sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
+  "sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
   "wham_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/wham:2024-01-24-v0.28.4-beta-9debd6d7",
   "igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
   "duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",
@@ -24,10 +24,10 @@
   "pangenie_docker": "us.gcr.io/broad-dsde-methods/vjalili/pangenie:vj-127571f",
   "sv-base-virtual-env": "us.gcr.io/broad-dsde-methods/vjalili/sv-base-virtual-env:5994670",
   "cnmops-virtual-env": "us.gcr.io/broad-dsde-methods/vjalili/cnmops-virtual-env:5994670",
-  "sv-pipeline-virtual-env": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline-virtual-env:2024-01-24-v0.28.4-beta-9debd6d7",
+  "sv-pipeline-virtual-env": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline-virtual-env:mw-train-genotype-filtering-a9479501",
   "samtools-cloud-virtual-env": "us.gcr.io/broad-dsde-methods/vjalili/samtools-cloud-virtual-env:5994670",
   "sv-utils-env": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils-env:2023-02-01-v0.26.8-beta-9b25c72d",
-  "sv_utils_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils:2024-01-24-v0.28.4-beta-9debd6d7",
+  "sv_utils_docker": "us.gcr.io/broad-dsde-methods/markw/sv-utils:mw-train-genotype-filtering-a9479501",
   "gq_recalibrator_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-tb-form-sv-filter-training-data-899360a",
   "str": "us.gcr.io/broad-dsde-methods/gatk-sv/str:2023-05-23-v0.27.3-beta-e537bdd6"
 }
diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json
@@ -2,20 +2,20 @@
   "name": "dockers",
   "cnmops_docker": "vahid.azurecr.io/gatk-sv/cnmops:2024-01-24-v0.28.4-beta-9debd6d7",
   "condense_counts_docker": "vahid.azurecr.io/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker": "vahid.azurecr.io/gatk-sv/gatk:2024-01-15-4.5.0.0-3-gb68fadc5f-NIGHTLY-SNAPSHOT",
+  "gatk_docker": "vahid.azurecr.io/gatk-sv/gatk:2024-02-16-4.5.0.0-8-gcfd4d87ec-NIGHTLY-SNAPSHOT",
   "gatk_docker_pesr_override": "vahid.azurecr.io/tsharpe/gatk:4.2.6.1-57-g9e03432",
   "genomes_in_the_cloud_docker": "vahid.azurecr.io/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "vahid.azurecr.io/google/ubuntu1804",
   "manta_docker": "vahid.azurecr.io/gatk-sv/manta:2023-09-14-v0.28.3-beta-3f22f94d",
-  "melt_docker": "vahid.azurecr.io/melt:3159ce1",
+  "melt_docker": "vahid.azurecr.io/melt:a85c92f",
   "scramble_docker": "vahid.azurecr.io/scramble:mw-scramble-99af4c50",
   "samtools_cloud_docker": "vahid.azurecr.io/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_docker": "vahid.azurecr.io/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_mini_docker": "vahid.azurecr.io/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_updates_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_qc_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_rdtest_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
+  "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
+  "sv_pipeline_updates_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
+  "sv_pipeline_qc_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
+  "sv_pipeline_rdtest_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-10c8a221",
   "wham_docker": "vahid.azurecr.io/gatk-sv/wham:2024-01-24-v0.28.4-beta-9debd6d7",
   "igv_docker": "vahid.azurecr.io/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
   "duphold_docker": "vahid.azurecr.io/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",

diff --git a/inputs/values/hgdp.json b/inputs/values/hgdp.json
@@ -32,9 +32,9 @@
   "concordance_vcf": "gs://gatk-sv-hgdp/mw-sv-concordance-update/hgdp.concordance.vcf.gz",
   "concordance_vcf_index": "gs://gatk-sv-hgdp/mw-sv-concordance-update/hgdp.concordance.vcf.gz.tbi",
 
-  "pacbio_sample_concordance_vcf": "gs://gatk-sv-hgdp/mw-sv-concordance-update/training/hgdp.concordance.subset.vcf.gz",
-  "pacbio_sample_concordance_vcf_index": "gs://gatk-sv-hgdp/mw-sv-concordance-update/training/hgdp.concordance.subset.vcf.gz.tbi",
-  "recalibrate_gq_truth_json": "gs://gatk-sv-hgdp/mw-sv-concordance-update/training/hgdp.gq_training_labels.json",
+  "pacbio_sample_concordance_vcf": "gs://gatk-sv-hgdp/mw-train-genotype-filtering/hgdp.pacbio_samples.vcf.gz",
+  "pacbio_sample_concordance_vcf_index": "gs://gatk-sv-hgdp/mw-train-genotype-filtering/hgdp.pacbio_samples.vcf.gz.tbi",
+  "recalibrate_gq_truth_json": "gs://gatk-sv-hgdp/mw-train-genotype-filtering/hgdp.gq_training_labels.json",
 
   "aou_recalibrated_vcf": "gs://gatk-sv-hgdp/mw-sv-concordance-update/hgdp.concordance.aou_gq_recalibrated.vcf.gz",
   "aou_recalibrated_vcf_index": "gs://gatk-sv-hgdp/mw-sv-concordance-update/hgdp.concordance.aou_gq_recalibrated.vcf.gz.tbi",