genomics-pipeline

Step 4: Structural Variant Calling (Manta)

What This Does

Detects large DNA changes (>50bp) that DeepVariant misses: deletions, duplications, inversions, translocations, and insertions.

Why

Structural variants cause ~25% of all genetic disease but are invisible to standard SNP/indel callers.

Tool

• Manta (Illumina) — structural variant and indel caller

Docker Image

quay.io/biocontainers/manta:1.6.0--h9ee0642_2

Command

SAMPLE=your_sample
GENOME_DIR=/path/to/your/data

# Step 1: Configure Manta
docker run --rm \
  --cpus 8 --memory 16g \
  -v ${GENOME_DIR}:/genome \
  quay.io/biocontainers/manta:1.6.0--h9ee0642_2 \
  configManta.py \
    --bam /genome/${SAMPLE}/aligned/${SAMPLE}_sorted.bam \
    --referenceFasta /genome/reference/Homo_sapiens_assembly38.fasta \
    --runDir /genome/${SAMPLE}/manta

# Step 2: Run Manta
docker run --rm \
  --cpus 8 --memory 16g \
  -v ${GENOME_DIR}:/genome \
  quay.io/biocontainers/manta:1.6.0--h9ee0642_2 \
  /genome/${SAMPLE}/manta/runWorkflow.py -j 8

# Output: diploidSV.vcf.gz (~7-9K structural variants)

Output

• results/variants/diploidSV.vcf.gz — main output (all SV calls)
• results/variants/candidateSV.vcf.gz — unfiltered candidates
• results/variants/candidateSmallIndels.vcf.gz — small indels

Important Notes

• Raw Manta output is UNFILTERED — most calls are benign
• Must run AnnotSV (step 5) to classify pathogenicity
• SVs >5MB in short-read WGS are usually artifacts from segmental duplications
• Typical results: 7,000-9,000 SVs per 30X WGS sample

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