diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..1ddda25 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "dpgt/DPGT"] + path = dpgt/DPGT + url = https://github.com/nttg8100/DPGT.git diff --git a/Readme.md b/Readme.md index 6f3ff94..9602a1e 100644 --- a/Readme.md +++ b/Readme.md @@ -4,5 +4,5 @@ Genomics Kit integrates the utilities for bioinformatics analysis 1. [igv-report](./igv-report): Generate the IGV report html format 2. [spark-on-slurm](./spark-on-slurm/): Spark on SLURM cluster configuration, supported - - [Hail](https://hail.is/): Powering genomic analysis, at every scale -3. [glnexus](https://github.com/dnanexus-rnd/GLnexus): The joint variant calling for cohort vcf for deepvariant gvcf +3. [GLnexus](https://github.com/dnanexus-rnd/GLnexus): The joint variant calling for cohort vcf for deepvariant gvcf +4. [DPGT](https://github.com/BGI-flexlab/DPGT): DPGT is a distributed population genetics analysis tool which enabled joint calling on millions of WGS(whole genome sequencing) samples. diff --git a/common.mk b/common.mk new file mode 100644 index 0000000..117d50a --- /dev/null +++ b/common.mk @@ -0,0 +1,3 @@ +.PHONY: test +${HOME}/.pixi/bin/pixi: + curl -sSL https://pixi.sh/install.sh | sh \ No newline at end of file diff --git a/dpgt/.gitignore b/dpgt/.gitignore new file mode 100644 index 0000000..9a10d9a --- /dev/null +++ b/dpgt/.gitignore @@ -0,0 +1,3 @@ +*.log +reference +build \ No newline at end of file diff --git a/dpgt/DPGT b/dpgt/DPGT new file mode 160000 index 0000000..bc88069 --- /dev/null +++ b/dpgt/DPGT @@ -0,0 +1 @@ +Subproject commit bc8806960f325d5c7aad0e287b28c5103b094d1c diff --git a/dpgt/Makefile b/dpgt/Makefile new file mode 100644 index 0000000..da8322b --- /dev/null +++ b/dpgt/Makefile @@ -0,0 +1,29 @@ +include ../common.mk +.PHONY: clone build build-cpp build-java clean prep-input run-verify +clone: + bash scripts/clone_DPGT.sh + +build: clone build-cpp build-java + @echo "DPGT fully built!" + +build-cpp: ${HOME}/.pixi/bin/pixi + mkdir -p build + @echo "Building C++ native libraries..." + ${HOME}/.pixi/bin/pixi run build-cpp + +build-java: ${HOME}/.pixi/bin/pixi + mkdir -p build + @echo "Building Java JAR package..." + cd DPGT && ${HOME}/.pixi/bin/pixi run mvn package -q -DskipTests + @echo "Java build complete!" + +test: build ${HOME}/.pixi/bin/pixi + ${HOME}/.pixi/bin/pixi run bash scripts/download.sh + ${HOME}/.pixi/bin/pixi run bash scripts/run_dpgt.sh + +clean: + @echo "Cleaning build artifacts..." + rm -rf build DPGT/target vcf_input.list results_cohort results* + @echo "Cleaned!" + +.DEFAULT_GOAL := help diff --git a/dpgt/Readme.md b/dpgt/Readme.md new file mode 100644 index 0000000..3307370 --- /dev/null +++ b/dpgt/Readme.md @@ -0,0 +1,36 @@ +# DPGT Cohort VCF (Pixi) + +Build and run DPGT locally with Pixi, then generate a joint-genotyped cohort VCF from 3 samples. + +## Quick Start + +```bash +pixi install +bash run_dpgt.sh +``` + +## What `run_dpgt.sh` does + +- checks DPGT jar and native library +- runs joint genotyping in local mode +- writes cohort VCF to an output directory + +Default output example: + +- `results_verify_1kgp_run_dpgt/result.chr12_111760000_111765000.0.vcf.gz` + +## Optional overrides + +```bash +INPUT_LIST=inputs/1kgp_3samples.list \ +REFERENCE_FASTA=reference/Homo_sapiens_assembly38.fasta \ +OUTPUT_DIR=results/my_run \ +TARGET_REGION=chr12:111760000-111765000 \ +JOBS=4 \ +bash run_dpgt.sh +``` + +## Notes + +- 1KGP 3-sample run is validated and produces cohort VCF. +- GIAB inputs may fail due to `` compatibility in genotyping. diff --git a/dpgt/cohort_vcf/.gitignore b/dpgt/cohort_vcf/.gitignore new file mode 100644 index 0000000..f7af633 --- /dev/null +++ b/dpgt/cohort_vcf/.gitignore @@ -0,0 +1,6 @@ +*.gz +*gz.tbi +GLnexus.DB +*.bcf +*.bed +results \ No newline at end of file diff --git a/dpgt/cohort_vcf/1KGP/data/.placeholder b/dpgt/cohort_vcf/1KGP/data/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/dpgt/cohort_vcf/1KGP/gvcf_input.list b/dpgt/cohort_vcf/1KGP/gvcf_input.list new file mode 100644 index 0000000..0b880b5 --- /dev/null +++ b/dpgt/cohort_vcf/1KGP/gvcf_input.list @@ -0,0 +1,3 @@ +cohort_vcf/1KGP/data/NA21142.final.hard-filtered.gvcf.gz +cohort_vcf/1KGP/data/NA21143.final.hard-filtered.gvcf.gz +cohort_vcf/1KGP/data/NA21144.final.hard-filtered.gvcf.gz diff --git a/dpgt/cohort_vcf/GIAB/data/.placeholder b/dpgt/cohort_vcf/GIAB/data/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/dpgt/cohort_vcf/GIAB/gvcf_input.list b/dpgt/cohort_vcf/GIAB/gvcf_input.list new file mode 100644 index 0000000..b94afc1 --- /dev/null +++ b/dpgt/cohort_vcf/GIAB/gvcf_input.list @@ -0,0 +1,3 @@ +cohort_vcf/GIAB/data/HG002.child.g.vcf.gz +cohort_vcf/GIAB/data/HG003.parent1.g.vcf.gz +cohort_vcf/GIAB/data/HG004.parent2.g.vcf.gz diff 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+awscliv2 = ">=2.3.1,<3" +google-cloud-storage = ">=3.10.1,<4" +gsutil = ">=5.36,<6" + +[tasks] +# Build C++ libraries +build-cpp = { cmd = "bash scripts/build_cpp.sh", depends-on = [], description = "Build C++ native libraries" } + +# Build Java package +build-java = { cmd = "cd DPGT && mvn package -q", depends-on = ["build-cpp"], description = "Build Java JAR package" } + +# Full build +build = { cmd = "echo 'Building DPGT...' && sleep 1", depends-on = ["build-cpp", "build-java"], description = "Full build (C++ + Java)" } + +# Create input VCF list file +prep-input = { cmd = "echo '/scratch/data/gkit/dpgt/cohort_vcf/1KGP/data/1KGP_ALDH2_5kb.bcf' > vcf_input.list && echo 'Created vcf_input.list with cohort VCF' && cat vcf_input.list", description = "Prepare input VCF list for DPGT" } + +# Run DPGT on cohort VCF (local mode) - verify build +run-local = { cmd = "export LD_LIBRARY_PATH=$(pwd)/build/lib:${LD_LIBRARY_PATH} && java -cp $(find DPGT/target -name 'dpgt*.jar' | head -1) org.bgi.flexlab.dpgt.jointcalling.JointCallingSpark --help || echo 'Build first with: pixi run build'", depends-on = ["build"], description = "Run DPGT help (verify build)" } + +# Clean build artifacts +clean = { cmd = "rm -rf build DPGT/target vcf_input.list results_cohort", description = "Clean build artifacts and outputs" } + +# Setup environment variables +setup = { cmd = "echo '=== DPGT Setup ===' && echo '' && echo 'Cohort VCF available at: /scratch/data/gkit/dpgt/cohort_vcf/1KGP/' && echo '' && echo 'Available tasks:' && echo ' pixi run build - Build DPGT (C++ + Java)' && echo ' pixi run prep-input - Create VCF input list' && echo ' pixi run run-local - Verify build (show DPGT help)' && echo ' pixi run clean - Clean artifacts' && echo '' && echo 'Full workflow:' && echo ' pixi run build && pixi run prep-input && pixi run run-local'", description = "Display setup information" } + diff --git a/dpgt/scripts/build_cpp.sh b/dpgt/scripts/build_cpp.sh new file mode 100755 index 0000000..10e6e58 --- /dev/null +++ b/dpgt/scripts/build_cpp.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -e + +echo "Building DPGT C++ libraries..." +mkdir -p build +cd build +cmake -DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" -DJAVA_INCLUDE_PATH="${JAVA_HOME}/include" ../DPGT/src/main/native/ +make -j 8 +echo "C++ build completed successfully!" diff --git a/dpgt/scripts/clone_DPGT.sh b/dpgt/scripts/clone_DPGT.sh new file mode 100755 index 0000000..1772371 --- /dev/null +++ b/dpgt/scripts/clone_DPGT.sh @@ -0,0 +1,46 @@ +#!/usr/bin/env bash +set -euo pipefail + +PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" +DPGT_DIR="${PROJECT_ROOT}/DPGT" +FORK_URL="${DPGT_FORK_URL:-https://github.com/nttg8100/DPGT.git}" + +echo "[clone] project root: ${PROJECT_ROOT}" +echo "[clone] fork url: ${FORK_URL}" + +if ! git -C "${PROJECT_ROOT}" rev-parse --is-inside-work-tree >/dev/null 2>&1; then + echo "[clone] ERROR: ${PROJECT_ROOT} is not a git repository" + exit 1 +fi + +echo "[clone] init top-level DPGT submodule" +git -C "${PROJECT_ROOT}" config submodule.DPGT.url "${FORK_URL}" +git -C "${PROJECT_ROOT}" submodule sync --recursive DPGT +git -C "${PROJECT_ROOT}" submodule update --init --recursive DPGT + +if [ ! -d "${DPGT_DIR}" ]; then + echo "[clone] ERROR: DPGT directory not found after init" + exit 1 +fi + +if [ -f "${DPGT_DIR}/.gitmodules" ]; then + echo "[clone] set DPGT origin to fork" + git -C "${DPGT_DIR}" remote set-url origin "${FORK_URL}" || true + + echo "[clone] rewrite nested submodule URLs to HTTPS" + sed -i 's#git@github.com:#https://github.com/#g' "${DPGT_DIR}/.gitmodules" + sed -i 's#git@gitlab.com:#https://gitlab.com/#g' "${DPGT_DIR}/.gitmodules" + + echo "[clone] sync nested submodule config" + git -C "${DPGT_DIR}" submodule sync --recursive + + echo "[clone] clear cached nested submodule metadata" + git -C "${DPGT_DIR}" submodule deinit -f --all || true + rm -rf "${DPGT_DIR}/.git/modules" + + echo "[clone] init nested DPGT submodules" + git -C "${DPGT_DIR}" submodule update --init --recursive +fi + +echo "[clone] done. nested submodule status:" +git -C "${DPGT_DIR}" submodule status --recursive || true diff --git a/dpgt/scripts/download.sh b/dpgt/scripts/download.sh new file mode 100755 index 0000000..eb7e9fd --- /dev/null +++ b/dpgt/scripts/download.sh @@ -0,0 +1,30 @@ +HOME_DIR=$(pwd) +################ Download data ############################## +# Download reference +mkdir -p reference +aws s3 cp --no-sign-request s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta reference +aws s3 cp --no-sign-request s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai reference +aws s3 cp --no-sign-request s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict reference + +# # GIAB: has error due to gvcf format +# cd ${HOME_DIR}/cohort_vcf/GIAB/data +# gsutil cp gs://deepvariant/case-study-outputs/1.10.0/deeptrio/wgs/HG002.child.g.vcf.gz . +# gsutil cp gs://deepvariant/case-study-outputs/1.10.0/deeptrio/wgs/HG002.child.g.vcf.gz.tbi . + +# gsutil cp gs://deepvariant/case-study-outputs/1.10.0/deeptrio/wgs/HG003.parent1.g.vcf.gz . +# gsutil cp gs://deepvariant/case-study-outputs/1.10.0/deeptrio/wgs/HG003.parent1.g.vcf.gz.tbi . + +# gsutil cp gs://deepvariant/case-study-outputs/1.10.0/deeptrio/wgs/HG004.parent2.g.vcf.gz . +# gsutil cp gs://deepvariant/case-study-outputs/1.10.0/deeptrio/wgs/HG004.parent2.g.vcf.gz.tbi . + + +# 1KGP +cd ${HOME_DIR}/cohort_vcf/1KGP/data +aws s3 cp --no-sign-request s3://1000genomes-dragen-v4-2-7/data/individuals/hg38_alt_masked_graph_v3/NA21144/NA21144.final.hard-filtered.gvcf.gz . +aws s3 cp --no-sign-request s3://1000genomes-dragen-v4-2-7/data/individuals/hg38_alt_masked_graph_v3/NA21144/NA21144.final.hard-filtered.gvcf.gz.tbi . + +aws s3 cp --no-sign-request s3://1000genomes-dragen-v4-2-7/data/individuals/hg38_alt_masked_graph_v3/NA21143/NA21143.final.hard-filtered.gvcf.gz . +aws s3 cp --no-sign-request s3://1000genomes-dragen-v4-2-7/data/individuals/hg38_alt_masked_graph_v3/NA21143/NA21143.final.hard-filtered.gvcf.gz.tbi . + +aws s3 cp --no-sign-request s3://1000genomes-dragen-v4-2-7/data/individuals/hg38_alt_masked_graph_v3/NA21142/NA21142.final.hard-filtered.gvcf.gz . +aws s3 cp --no-sign-request s3://1000genomes-dragen-v4-2-7/data/individuals/hg38_alt_masked_graph_v3/NA21142/NA21142.final.hard-filtered.gvcf.gz.tbi . \ No newline at end of file diff --git a/dpgt/scripts/run_dpgt.sh b/dpgt/scripts/run_dpgt.sh new file mode 100755 index 0000000..bced74c --- /dev/null +++ b/dpgt/scripts/run_dpgt.sh @@ -0,0 +1,92 @@ +#!/bin/bash +# DPGT runner for joint genotyping cohort VCF + +set -euo pipefail + +PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" +BUILD_LIB_PATH="${PROJECT_ROOT}/build/lib" +DPGT_JAR="${PROJECT_ROOT}/DPGT/target/dpgt-1.3.2.0.jar" + +# Defaults (override with env vars if needed) +INPUT_LIST="${INPUT_LIST:-${PROJECT_ROOT}/cohort_vcf/1KGP/gvcf_input.list}" +REFERENCE_FASTA="${REFERENCE_FASTA:-${PROJECT_ROOT}/reference/Homo_sapiens_assembly38.fasta}" +OUTPUT_DIR="${OUTPUT_DIR:-${PROJECT_ROOT}/cohort_vcf/1KGP/results}" +TARGET_REGION="${TARGET_REGION:-chr12:111760000-111763759}" +JOBS="${JOBS:-4}" +ALLOW_OVERWRITE="${ALLOW_OVERWRITE:-0}" + +echo "================================" +echo "DPGT Cohort VCF Runner" +echo "================================" +echo "" + +# Check prerequisites +echo "Checking prerequisites..." +if [ -z "$DPGT_JAR" ] || [ ! -f "$DPGT_JAR" ]; then + echo "ERROR: DPGT JAR not found at $DPGT_JAR" + echo "Run 'make build' to compile DPGT first" + exit 1 +fi + +if [ ! -f "$BUILD_LIB_PATH/libcdpgt.so" ]; then + echo "ERROR: libcdpgt.so not found at $BUILD_LIB_PATH" + echo "Run 'make build-cpp' to compile C++ libraries" + exit 1 +fi + +if [ ! -f "$INPUT_LIST" ]; then + echo "ERROR: input list not found: $INPUT_LIST" + echo "Create it with one gVCF path per line (3-sample trio supported)." + echo "Example existing list: ${PROJECT_ROOT}/gvcf_input.list" + exit 1 +fi + +if [ ! -f "$REFERENCE_FASTA" ]; then + echo "ERROR: reference fasta not found: $REFERENCE_FASTA" + exit 1 +fi + +if [ -d "$OUTPUT_DIR" ] && [ "$(ls -A "$OUTPUT_DIR" 2>/dev/null || true)" != "" ]; then + if [ "$ALLOW_OVERWRITE" = "1" ]; then + echo "Output exists. Removing: $OUTPUT_DIR" + rm -rf "$OUTPUT_DIR" + else + echo "ERROR: output directory exists and is not empty: $OUTPUT_DIR" + echo "Set ALLOW_OVERWRITE=1 or choose another OUTPUT_DIR" + exit 1 + fi +fi + +echo "DPGT JAR: $DPGT_JAR" +echo "C++ Library: $BUILD_LIB_PATH/libcdpgt.so" +echo "Input List: $INPUT_LIST" +echo "Reference: $REFERENCE_FASTA" +echo "Output Dir: $OUTPUT_DIR" +echo "Region: $TARGET_REGION" +echo "" +echo "Note: default region is a small smoke-test interval." +echo "" + +# Runtime environment +export LD_LIBRARY_PATH="$BUILD_LIB_PATH:${LD_LIBRARY_PATH:-}" + +echo "Running DPGT joint genotyping..." +echo "" + +# Some environments need explicit local filesystem implementations for Spark/Hadoop +java \ + -Dspark.hadoop.fs.file.impl=org.apache.hadoop.fs.LocalFileSystem \ + -Dspark.hadoop.fs.AbstractFileSystem.file.impl=org.apache.hadoop.fs.local.LocalFs \ + -cp "$DPGT_JAR" \ + org.bgi.flexlab.dpgt.jointcalling.JointCallingSpark \ + -i "$INPUT_LIST" \ + -r "$REFERENCE_FASTA" \ + -o "$OUTPUT_DIR" \ + -j "$JOBS" \ + -l "$TARGET_REGION" \ + --local + +echo "" +echo "Run complete." +echo "Output files in: $OUTPUT_DIR" +find "$OUTPUT_DIR" -maxdepth 1 -type f -name "result*.vcf.gz" -print || true