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14-imputation-prep.md

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Step 14: Imputation Preparation

What This Does

Prepares a WGS VCF for submission to the Michigan Imputation Server (MIS) or TOPMed Imputation Server. Splits the VCF by chromosome, filters to PASS variants, and converts to the required format.

Why

Imputation servers statistically infer missing genotypes using large reference panels. For WGS data, imputation is primarily useful for phasing (determining which alleles are on the same chromosome) rather than filling in missing variants. Phased data is required for haplotype-level analyses and accurate PRS calculation.

Tool

  • bcftools (samtools/bcftools) — for VCF filtering, splitting, and indexing

Docker Image

staphb/bcftools:1.21

Command

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

# Step 1: Filter to PASS variants only
docker run --rm \
  -v ${GENOME_DIR}/${SAMPLE}/vcf:/data \
  staphb/bcftools:1.21 \
  bcftools view -f PASS \
    /data/${SAMPLE}.vcf.gz \
    -Oz -o /data/${SAMPLE}_pass.vcf.gz

# Step 2: Index the filtered VCF
docker run --rm \
  -v ${GENOME_DIR}/${SAMPLE}/vcf:/data \
  staphb/bcftools:1.21 \
  bcftools index -t /data/${SAMPLE}_pass.vcf.gz

# Step 3: Split by chromosome (chr1-22, autosomes only)
for CHR in $(seq 1 22); do
  docker run --rm \
    -v ${GENOME_DIR}/${SAMPLE}/vcf:/data \
    staphb/bcftools:1.21 \
    bcftools view -r chr${CHR} \
      /data/${SAMPLE}_pass.vcf.gz \
      -Oz -o /data/imputation/chr${CHR}.vcf.gz

  docker run --rm \
    -v ${GENOME_DIR}/${SAMPLE}/vcf:/data \
    staphb/bcftools:1.21 \
    bcftools index -t /data/imputation/chr${CHR}.vcf.gz
done

# Output: 22 per-chromosome VCF files in /data/imputation/

Server Options

Server Panel Samples Build URL
Michigan (MIS) HRC r1.1 32,470 GRCh37/38 imputationserver.sph.umich.edu
TOPMed TOPMed r2 132,070 GRCh38 native imputation.biodatacatalyst.nhlbi.nih.gov

Important Notes

  • MIS requires a minimum of 20 samples per job — a single WGS sample is useful mainly for phasing, not imputation
  • TOPMed r2 panel is recommended for European ancestry (132K samples, GRCh38 native — no liftover needed)
  • Registration is required at the imputation server before submitting jobs
  • Upload per-chromosome VCF files (not the whole-genome file)
  • Servers accept .vcf.gz format — ensure files are bgzipped (bcftools output is bgzipped by default)
  • Sex chromosomes (chrX) can be submitted separately with ploidy-aware settings
  • Results include phased haplotypes and imputation quality scores (R-squared) — filter imputed variants with R2 < 0.3
  • Create the output directory before running: mkdir -p ${GENOME_DIR}/${SAMPLE}/vcf/imputation