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tasks/multisample-variants/run_script.sh

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+#!/bin/bash
+set -e
+
+# =============================================================================
+# Task 24: Multi-sample Variant Calling and Comparison
+#
+# DAG (depth 6, per-sample parallel then merge):
+#
+# L0: reads_A + reads_B + reference
+# L1: fastp A          fastp B
+# L2: bwa A            bwa B
+# L3: freebayes A      freebayes B
+# L4: bcftools filter A  bcftools filter B
+#     └──────────┬───────────┘
+# L5: bcftools isec (shared vs unique variants)
+#     └── variant annotation + summary
+# L6: MERGE
+# =============================================================================
+
+THREADS=$(( $(nproc) > 8 ? 8 : $(nproc) ))
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+DATA="${SCRIPT_DIR}/data"
+REF="${SCRIPT_DIR}/reference"
+OUT="${SCRIPT_DIR}/outputs"
+RES="${SCRIPT_DIR}/results"
+
+REFERENCE="${REF}/reference.fna"
+SAMPLES=("sampleA" "sampleB")
+
+log_step() {
+    echo "=================================================================="
+    echo "STEP: $1"
+    echo "$(date)"
+    echo "=================================================================="
+}
+
+mkdir -p "${OUT}"/{trimmed,aligned,variants,filtered,comparison} "${RES}"
+
+# Per-sample processing (L1-L4)
+for SAMPLE in "${SAMPLES[@]}"; do
+    # L1: Trim
+    log_step "L1: fastp ${SAMPLE}"
+    if [ ! -f "${OUT}/trimmed/${SAMPLE}_R1.fastq.gz" ]; then
+        fastp --in1 "${DATA}/${SAMPLE}_R1.fastq.gz" --in2 "${DATA}/${SAMPLE}_R2.fastq.gz" \
+              --out1 "${OUT}/trimmed/${SAMPLE}_R1.fastq.gz" --out2 "${OUT}/trimmed/${SAMPLE}_R2.fastq.gz" \
+              --detect_adapter_for_pe --thread ${THREADS} \
+              --json "${OUT}/trimmed/${SAMPLE}_fastp.json"
+    else echo "Skipping (exists)"; fi
+
+    # L2: Align
+    log_step "L2: bwa ${SAMPLE}"
+    if [ ! -f "${OUT}/aligned/${SAMPLE}.bam" ]; then
+        [ ! -f "${REFERENCE}.bwt" ] && bwa index "${REFERENCE}" 2>/dev/null
+        bwa mem -t ${THREADS} -R "@RG\tID:${SAMPLE}\tSM:${SAMPLE}\tPL:ILLUMINA" \
+                "${REFERENCE}" "${OUT}/trimmed/${SAMPLE}_R1.fastq.gz" "${OUT}/trimmed/${SAMPLE}_R2.fastq.gz" \
+            | samtools sort -@ ${THREADS} -o "${OUT}/aligned/${SAMPLE}.bam"
+        samtools index "${OUT}/aligned/${SAMPLE}.bam"
+    else echo "Skipping (exists)"; fi
+
+    # L3: Call variants
+    log_step "L3: freebayes ${SAMPLE}"
+    if [ ! -f "${OUT}/variants/${SAMPLE}.vcf" ]; then
+        freebayes -f "${REFERENCE}" "${OUT}/aligned/${SAMPLE}.bam" \
+                  --min-mapping-quality 20 --min-base-quality 20 \
+                  > "${OUT}/variants/${SAMPLE}.vcf"
+    else echo "Skipping (exists)"; fi
+
+    # L4: Filter
+    log_step "L4: bcftools filter ${SAMPLE}"
+    if [ ! -f "${OUT}/filtered/${SAMPLE}.vcf.gz" ]; then
+        bcftools filter -i 'QUAL>20 && INFO/DP>5' "${OUT}/variants/${SAMPLE}.vcf" \
+            | bcftools view -Oz -o "${OUT}/filtered/${SAMPLE}.vcf.gz"
+        bcftools index "${OUT}/filtered/${SAMPLE}.vcf.gz"
+    else echo "Skipping (exists)"; fi
+done
+
+# L5: Compare variants between samples
+log_step "L5: bcftools isec (shared vs unique)"
+if [ ! -d "${OUT}/comparison/isec" ]; then
+    bcftools isec -p "${OUT}/comparison/isec" \
+                  "${OUT}/filtered/sampleA.vcf.gz" \
+                  "${OUT}/filtered/sampleB.vcf.gz"
+else echo "Skipping (exists)"; fi
+
+# Parse comparison results
+UNIQUE_A=$(grep -cv "^#" "${OUT}/comparison/isec/0000.vcf" 2>/dev/null || echo "0")
+UNIQUE_B=$(grep -cv "^#" "${OUT}/comparison/isec/0001.vcf" 2>/dev/null || echo "0")
+SHARED=$(grep -cv "^#" "${OUT}/comparison/isec/0002.vcf" 2>/dev/null || echo "0")
+
+# Per-sample stats
+VARS_A=$(bcftools stats "${OUT}/filtered/sampleA.vcf.gz" | grep "^SN" | grep "number of records" | cut -f4)
+VARS_B=$(bcftools stats "${OUT}/filtered/sampleB.vcf.gz" | grep "^SN" | grep "number of records" | cut -f4)
+SNPS_A=$(bcftools stats "${OUT}/filtered/sampleA.vcf.gz" | grep "^SN" | grep "number of SNPs" | cut -f4)
+SNPS_B=$(bcftools stats "${OUT}/filtered/sampleB.vcf.gz" | grep "^SN" | grep "number of SNPs" | cut -f4)
+
+# L6: MERGE
+log_step "L6-MERGE"
+
+cat > "${RES}/variant_comparison.csv" << CSVEOF
+metric,value
+total_variants_sampleA,${VARS_A}
+total_variants_sampleB,${VARS_B}
+snps_sampleA,${SNPS_A}
+snps_sampleB,${SNPS_B}
+unique_to_sampleA,${UNIQUE_A}
+unique_to_sampleB,${UNIQUE_B}
+shared_variants,${SHARED}
+CSVEOF
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/variant_comparison.csv"