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name: trio-calling description: "Plans DeepTrio trio and duo variant-calling workflows with child and parent inputs, per-sample VCF/gVCF outputs, and GLnexus merge handoff." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

DeepTrio Trio Calling

Use this sub-skill when a user needs DeepTrio family calling for a child with one or two parents. It covers Docker/Bazel-style run_deeptrio command planning, duo behavior when one parent is absent, model-type choice, per-sample output planning, gVCF merge handoff, and family-specific troubleshooting.

Route The Request

• Use this sub-skill for DeepTrio run_deeptrio workflows, trio/duo sample planning, child/parent output naming, gVCF planning, GLnexus handoff, and sex-chromosome parent-selection caveats.
• Route single-sample run_deepvariant germline calling to the germline-calling sub-skill.
• Route pangenome-aware DeepVariant workflows to the pangenome-aware-calling sub-skill.
• Route low-level make_examples, call_variants, postprocess_variants, sharded TFRecords, and extra-args internals to the pipeline-stages sub-skill.
• Route benchmarking reports, Mendelian-violation analysis, hap.py, RTG, and visualization to the analysis-visualization sub-skill.

Fast Path

1. Identify family mode: trio has child, parent1, and parent2; duo has child and exactly one parent.
2. Choose --model_type from WGS, WES, PACBIO, or ONT according to the sequencing data and image/model availability.
3. Require an indexed FASTA and sorted, indexed, compatible BAMs for every supplied sample.
4. Require one VCF output for every supplied sample, and request a matching gVCF for every supplied sample when GLnexus or cohort merging is planned.
5. Use scripts/deeptrio_command_builder.py to validate the plan and print a reviewable command without executing Docker, DeepTrio, or GLnexus.
6. Read references/workflows.md, references/deeptrio-flags.md, and references/troubleshooting.md for command patterns, flag contracts, and recovery steps.

Bundled Helper

The helper is a command planner only:

python scripts/deeptrio_command_builder.py --help

It validates child/parent flag groups, makes duo mode explicit by omitting every parent2 flag, warns about WES regions and long-read candidate partitioning, and can emit a GLnexus handoff command when a complete gVCF set is present.

Safety

Do not run Docker, GLnexus, network downloads, GPU jobs, or native DeepTrio tests without explicit user approval and real user-provided genomics inputs. Treat generated commands as plans until the user confirms the runtime environment, container mounts, and data paths.