domains / families / science / deepvariant

deepvariant

combined

Calls germline SNPs and indels with Google DeepVariant, which reframes variant calling as CNN image classification over multi-channel pileup tensors. Covers platform-specific model selection (WGS, WES, PACBIO, ONT_R104, HYBRID_PACBIO_ILLUMINA), one-shot run_deepvariant vs the three-stage make_examples/call_variants/postprocess_variants pipeline, GPU acceleration of call_variants, DeepTrio for family/trio and de-novo calling, and joint genotyping of gVCFs with GLnexus (not GenotypeGVCFs). Use when deciding DeepVariant vs GATK vs DRAGEN, picking the right --model_type for a sequencing platform, avoiding post-hoc GATK hard filters or BQSR that degrade CNN calls, calling de-novo variants in a trio, merging a DeepVariant cohort, or weighing GIAB-trained benchmark accuracy before clinical deployment.

When to use

• **DeepVariant** -- best indel accuracy and best difficult-region/long-read performance among open tools; generalizes across platforms with a model swap; needs no filter tuning. Default choice for indels, difficult regions, and long reads.
• **GATK HaplotypeCaller** -- every parameter auditable, mature joint calling with reference-confidence squaring-off, and regulatory precedent. Prefer for very large cohorts needing GenomicsDB scaling or clinical pipelines already validated…
• **DRAGEN** -- FPGA-accelerated, ~20-25 min per 30x genome, wins the difficult-to-map benchmarks; prefer for throughput when the hardware or cloud is available (subject to the GIAB-overfitting caveat below).

Skill page

Conflict

The two skills cover the same core DeepVariant workflow but contain material, non-overlapping guidance. The first copy (OpenClaw) provides concrete, copy-pasteable commands for installation, the three-stage pipeline, GPU acceleration, platform-specific runs, GLnexus joint calling, quality metrics, and a complete workflow script. The second copy (GPTomics) provides critical conceptual constraints and decision logic that the first lacks: the prohibition against applying GATK hard filters/VQSR to DeepVariant output, the recommendation to skip BQSR, the distinction between germline and somatic calling, and a detailed model selection table explaining failure modes. It also includes version compatibility checks. Combining them is necessary to avoid hiding the critical 'do not filter' constraint or the specific command templates.