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WES/WGS Cohort Joint-Genotyping Pipeline

A user-oriented guide for multi-sample joint genotyping using GenomicsDB, GenotypeGVCFs, and VQSR.

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Diagram: Cohort Joint-Genotyping Workflow​

WES/WGS cohort joint-genotyping workflow

Purpose​

This pipeline combines many per-sample gVCFs and performs cohort-level joint genotyping, producing a single VCF for all samples with consistent genotype calls and variant filtering.

Use this when:

  • You want consistent genotypes across a family or population.
  • You plan to build VQSR models on cohort-level variant distributions.
  • You are preparing a joint VCF for association or segregation analyses.

Inputs​

  • Sample map file (--sample-map):
    TSV used by GenomicsDBImport (sample name → gVCF path).
  • Per-sample gVCFs from the single-sample pipeline.
  • Reference genome (REF from env.sh).
  • VQSR resources (SNP and INDEL training sets).
  • Optional interval list for WES mode.

Workflow​

1. GenomicsDBImport​

  • Imports all gVCFs into a GenomicsDB workspace.
  • Handles both WES (interval-limited) and WGS (whole genome) modes.
  • Output: on-disk database accessed as gendb://<workspace>.

2. Joint Genotyping (GenotypeGVCFs)​

  • Runs GenotypeGVCFs on gendb://<workspace> and the reference.

  • Produces the cohort-level VCF:

    • cohort.gv.raw.vcf.gz

3. Count Variants and Decide on VQSR​

  • Counts SNPs and INDELs in the raw cohort VCF.
  • Compares counts to configurable thresholds:
    • MIN_SNP_FOR_VQSR (default 1000)
    • MIN_INDEL_FOR_VQSR (default 8000)
  • Determines whether to build SNP and/or INDEL VQSR models.

4. Build VQSR SNP Model​

  • If enough SNPs:
    • Run VariantRecalibrator in SNP mode.
    • Uses training resources and multiple annotations:
      • QD, FS, MQ, MQRankSum, ReadPosRankSum.
    • Outputs:
      • cohort.snp.recal.vcf.gz
      • cohort.snp.tranches.txt.

5. Build VQSR INDEL Model​

  • If enough INDELs:
    • Run VariantRecalibrator in INDEL mode.
    • Uses annotations:
      • QD, FS, ReadPosRankSum.
    • Outputs:
      • cohort.indel.recal.vcf.gz
      • cohort.indel.tranches.txt.

6. Apply VQSR​

  • If SNP model exists:
    • Apply SNP VQSR → cohort.post_snp.vcf.gz.
  • If INDEL model exists:
    • Apply INDEL VQSR → cohort.vqsr.vcf.gz.

The best available VCF (VQSR-filtered or raw) is used as input to the next step.

7. Hard Filtering and QC VCF​

  • Run VariantFiltration with a set of hard filters on:
    • QUAL, QD, FS, MQ, MQRankSum, ReadPosRankSum.
  • Output: cohort.gv.QC.vcf.gz.

This QC VCF is the primary cohort workflow output for downstream tools and project-level review.

Output Files​

FileDescription
cohort.gv.raw.vcf.gzRaw cohort joint-genotyped VCF
cohort.snp.recal.vcf.gzSNP VQSR model VCF
cohort.snp.tranches.txtSNP VQSR tranches and diagnostics
cohort.indel.recal.vcf.gzINDEL VQSR model VCF
cohort.indel.tranches.txtINDEL VQSR tranches and diagnostics
cohort.post_snp.vcf.gzVCF after applying SNP VQSR
cohort.vqsr.vcf.gzVCF after applying SNP and INDEL VQSR
cohort.gv.QC.vcf.gzFinal hard-filtered cohort QC VCF (recommended)
logs/cohort_joint_genotyping.logMain log file for the cohort pipeline

When to Use This Pipeline​

  • After you have gVCFs from the single-sample pipeline.
  • When you need a single VCF for all samples for:
    • Family-based segregation analysis.
    • Case/control or population cohorts.
    • Downstream tools that expect joint genotypes.