From 25a6c1ae3232b8babb01d0ccffd0fd10533f61b1 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:47:03 +0000 Subject: [PATCH 1/9] [upstream-sync] scientific-skills/research-grants/references/budget_preparation.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/budget_preparation.md | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/budget_preparation.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/budget_preparation.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/budget_preparation.md new file mode 100644 index 00000000..281375d7 --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/budget_preparation.md @@ -0,0 +1,55 @@ +--- +title: "Budget Preparation for Research Grants" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/budget_preparation.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Budget Preparation for Research Grants + +## Purpose + +The budget translates the research plan into a credible resource plan. Reviewers and program staff use it to judge whether the scope, staffing, timeline, and requested funds are aligned. + +## Core Budget Categories + +- **Personnel**: PI, co-investigators, staff, postdocs, students, consultants, and fringe benefits. +- **Equipment**: Durable items that meet the agency and institutional equipment threshold. +- **Materials and supplies**: Consumables, reagents, software, cloud credits, and lab supplies. +- **Travel**: Fieldwork, collaboration visits, required meetings, and conference dissemination. +- **Participant or patient costs**: Recruitment, incentives, clinical costs, and related services. +- **Publication and dissemination**: Open-access fees, data hosting, workshops, and outreach. +- **Subawards**: Collaborating institution work with their own direct and indirect costs. +- **Indirect costs**: Facilities and administrative costs under the institutional negotiated rate. + +## Preparation Workflow + +1. Build the work breakdown from aims, tasks, milestones, and deliverables. +2. Map each task to people, effort, supplies, services, equipment, and travel. +3. Check agency caps, unallowable costs, cost-sharing rules, and budget format. +4. Validate institutional rates for salary escalation, fringe, tuition, and indirect costs. +5. Reconcile the budget against the narrative, timeline, biosketches, and facilities section. + +## Budget Justification Checklist + +- Every major cost is necessary for a named task or milestone. +- Personnel effort matches roles described in the project plan. +- Equipment requests explain why existing resources are insufficient. +- Travel has a clear project purpose, not generic conference attendance. +- Subawards include a distinct scope of work and responsible lead. +- Year-to-year changes are explained. +- Cost sharing is included only when required or strategically justified. + +## Common Pitfalls + +- Asking for resources not mentioned in the research strategy. +- Under-budgeting staff time for data management, compliance, or coordination. +- Omitting publication, computing, storage, animal, participant, or core facility costs. +- Using unexplained round numbers. +- Ignoring agency-specific caps or modular budget constraints. -- 2.54.0 From 6c88797774580eac83483a3fabc1f4c72ae99950 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:47:16 +0000 Subject: [PATCH 2/9] [upstream-sync] scientific-skills/research-grants/references/funding_mechanisms.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/funding_mechanisms.md | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/funding_mechanisms.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/funding_mechanisms.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/funding_mechanisms.md new file mode 100644 index 00000000..5eb869ab --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/funding_mechanisms.md @@ -0,0 +1,55 @@ +--- +title: "Funding Mechanisms Overview" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/funding_mechanisms.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Funding Mechanisms Overview + +## NIH + +- **R01**: Mature research project, typically 3-5 years, substantial preliminary data expected. +- **R21**: Exploratory or high-risk work, shorter and smaller than an R01. +- **R03**: Small grants for limited-scope projects. +- **K awards**: Career development awards with mentoring and training plans. +- **F awards**: Individual fellowships for predoctoral or postdoctoral trainees. +- **U mechanisms**: Cooperative agreements with substantial NIH program involvement. + +## NSF + +- **Core research programs**: Investigator-initiated proposals within directorate programs. +- **CAREER**: Early-career faculty award integrating research and education. +- **EAGER**: Exploratory, high-risk, potentially transformative work. +- **RAPID**: Urgent research with time-sensitive opportunity. +- **Center or institute programs**: Larger, collaborative, multi-investigator efforts. + +## DOE + +- **Office of Science FOAs**: Basic research aligned with office priorities. +- **Early Career Research Program**: Support for outstanding early-career scientists. +- **ARPA-E**: High-risk energy technology with commercialization or transition potential. +- **National laboratory collaborations**: Mechanisms involving DOE lab capabilities or user facilities. + +## DARPA + +- **BAA responses**: Program-specific proposals against broad agency announcements. +- **Seedlings or exploratory calls**: Shorter early-stage efforts when available. +- **Young Faculty Award**: Early-career faculty with high-risk ideas relevant to DARPA. + +## Selection Guidance + +Choose a mechanism by matching: + +- Project maturity and preliminary data. +- Risk level and expected payoff. +- Team career stage. +- Budget and duration needs. +- Agency mission fit. +- Review culture and success criteria. -- 2.54.0 From b2f62b3b20f0caff6c691116713783e6d1c6a99d Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:47:34 +0000 Subject: [PATCH 3/9] [upstream-sync] scientific-skills/research-grants/references/research_methods.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/research_methods.md | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/research_methods.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/research_methods.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/research_methods.md new file mode 100644 index 00000000..4d26db1a --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/research_methods.md @@ -0,0 +1,50 @@ +--- +title: "Research Methods in Grant Proposals" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/research_methods.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Research Methods in Grant Proposals + +## Purpose + +The methods section persuades reviewers that the proposed work can answer the research question with rigor, feasibility, and appropriate controls. + +## Essential Components + +- Study design or experimental design. +- Data sources, samples, subjects, systems, or models. +- Inclusion, exclusion, randomization, blinding, and control conditions where relevant. +- Measurements, instruments, assays, algorithms, or protocols. +- Statistical or computational analysis plan. +- Power, sample size, uncertainty, and sensitivity analysis where appropriate. +- Rigor, reproducibility, validation, and quality control. +- Alternative approaches for the most likely failure modes. + +## Experimental Research + +Describe biological or physical systems, controls, replicates, reagents, equipment, outcome measures, and analysis methods. Make clear which data support each hypothesis or aim. + +## Computational Research + +Describe datasets, preprocessing, model design, baselines, validation splits, metrics, error analysis, compute resources, software availability, and reproducibility plan. + +## Clinical or Translational Research + +Describe population, recruitment, consent, intervention or exposure, endpoints, monitoring, safety, regulatory approvals, and statistical analysis. + +## Reviewer Checks + +- Does each aim have a concrete method? +- Are controls and comparisons sufficient? +- Are sample sizes justified? +- Are assumptions explicit? +- Are risks and alternatives credible? +- Can another expert reproduce the work from the description? -- 2.54.0 From 3733bfdb8669ab63fbbf01b9a6402fae7fb14d5a Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:47:51 +0000 Subject: [PATCH 4/9] [upstream-sync] scientific-skills/research-grants/references/resubmission_strategies.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/resubmission_strategies.md | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/resubmission_strategies.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/resubmission_strategies.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/resubmission_strategies.md new file mode 100644 index 00000000..c5276142 --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/resubmission_strategies.md @@ -0,0 +1,54 @@ +--- +title: "Resubmission Strategies" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/resubmission_strategies.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Resubmission Strategies + +## Purpose + +A resubmission should show that the team understood reviewer concerns, made substantive improvements, and preserved the proposal's central value. + +## First Step + +Read the reviews in three passes: + +1. Identify fatal concerns versus fixable presentation issues. +2. Group comments by theme: significance, innovation, approach, team, environment, budget. +3. Decide whether to revise, redirect to another mechanism, or build more preliminary data first. + +## NIH A1 Resubmissions + +- Use the introduction page to summarize major changes. +- Address all major critiques respectfully and specifically. +- Make changes visible through rewritten sections, not track changes. +- Strengthen preliminary data, rigor, statistics, or alternatives where requested. +- Do not argue with reviewers unless correcting a factual misunderstanding. + +## NSF Resubmissions + +NSF has no universal formal introduction page. Incorporate reviewer feedback into the revised narrative, especially around intellectual merit, broader impacts, feasibility, and clarity. + +## Strong Response Patterns + +- "We clarified..." for communication problems. +- "We added preliminary data..." for feasibility concerns. +- "We revised Aim 2..." for design concerns. +- "We added an alternative strategy..." for risk concerns. +- "We recruited collaborator X..." for expertise gaps. + +## When Not to Resubmit Immediately + +- Reviewers rejected the premise rather than the execution. +- The mechanism or program fit was poor. +- Essential preliminary data are missing. +- The team lacks required expertise. +- The budget or timeline is not credible without scope reduction. -- 2.54.0 From 9b856d6f196bf400d52a86d9fd69183f8cbdf210 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:48:05 +0000 Subject: [PATCH 5/9] [upstream-sync] scientific-skills/research-grants/references/review_criteria.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/review_criteria.md | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/review_criteria.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/review_criteria.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/review_criteria.md new file mode 100644 index 00000000..5dfa205c --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/review_criteria.md @@ -0,0 +1,58 @@ +--- +title: "Comparative Review Criteria" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/review_criteria.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Comparative Review Criteria + +## NSF + +NSF proposals are reviewed on **Intellectual Merit** and **Broader Impacts**. Strong proposals make both criteria explicit in the project summary, project description, and evaluation plan. + +- Intellectual Merit: importance, originality, technical rigor, qualifications, and resources. +- Broader Impacts: societal benefit, education, workforce development, participation, dissemination, and infrastructure. + +## NIH + +Most NIH research project grants receive an overall impact score informed by five scored criteria. + +- Significance: importance of the problem and likely impact. +- Investigator(s): expertise, productivity, and team suitability. +- Innovation: conceptual, technical, or methodological novelty. +- Approach: rigor, feasibility, alternatives, statistics, and risk handling. +- Environment: institutional support, facilities, and collaborative setting. + +Reviewers also assess protections for human subjects, vertebrate animals, biohazards, authentication, data management, and rigor and reproducibility. + +## DOE + +DOE review criteria vary by office and FOA, but commonly emphasize scientific and technical merit, relevance to program mission, applicant qualifications, adequacy of resources, and reasonableness of budget. + +Competitive DOE proposals connect the scientific question to the office mission, national laboratory or user facility context when relevant, and measurable outcomes. + +## DARPA + +DARPA reviews focus on whether the work attacks a DARPA-hard problem with high payoff, credible technical milestones, and a path to transition. + +- Technical innovation and risk. +- Potential impact if successful. +- Measurable milestones and demonstration plan. +- Team capability and execution speed. +- Transition relevance to defense or national-security users. + +## Cross-Agency Reviewer Questions + +- What important problem does this solve? +- Why is now the right time? +- Why is this team the right team? +- What makes the approach credible? +- What can go wrong, and what is the fallback? +- What will be true at the end of the award that is not true today? -- 2.54.0 From 8ab9fdbd0aeafa395f689fd8ec97404e9374163b Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:48:15 +0000 Subject: [PATCH 6/9] [upstream-sync] scientific-skills/research-grants/references/team_building.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/team_building.md | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/team_building.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/team_building.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/team_building.md new file mode 100644 index 00000000..1acc1617 --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/team_building.md @@ -0,0 +1,52 @@ +--- +title: "Team Building for Research Grants" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/team_building.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Team Building for Research Grants + +## Purpose + +The team section should convince reviewers that the proposed work has the right expertise, leadership, collaboration structure, and institutional support. + +## Team Design Questions + +- What expertise is essential for each aim? +- Which roles must be senior investigators versus staff or trainees? +- Where are the methodological, clinical, computational, or translational gaps? +- What facilities, cores, field sites, datasets, or partnerships are required? +- Who owns coordination, data management, compliance, and dissemination? + +## Roles to Define + +- Principal investigator or project lead. +- Co-investigators and senior/key personnel. +- Collaborators and consultants. +- Project manager or coordinator. +- Data, software, statistics, or evaluation leads. +- Trainees and mentoring structure. +- External advisory board, if appropriate. + +## Evidence of Fit + +- Prior publications or preliminary data in the area. +- Complementary expertise across aims. +- Prior collaboration or a clear collaboration plan. +- Letters that commit specific resources or activities. +- Institutional support, facilities, and protected time. + +## Common Pitfalls + +- Adding famous names without defined roles. +- Missing key expertise for a high-risk method. +- Overloading the PI with all tasks. +- Providing generic letters of support. +- Failing to explain how multi-site coordination will work. -- 2.54.0 From 0a9ea1eb64245a4318ea4e88889b383de8d128ed Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:48:29 +0000 Subject: [PATCH 7/9] [upstream-sync] scientific-skills/research-grants/references/timeline_planning.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../references/timeline_planning.md | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/timeline_planning.md diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/timeline_planning.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/timeline_planning.md new file mode 100644 index 00000000..0d8582f1 --- /dev/null +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/scientific-skills/research-grants/references/timeline_planning.md @@ -0,0 +1,51 @@ +--- +title: "Timeline Planning for Research Grants" +task: "" +lineage_type: import +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/scientific-skills/research-grants/references/timeline_planning.md +upstream_sha: 708d419d +imported_at: 2026-07-13 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Timeline Planning for Research Grants + +## Purpose + +A timeline shows that the project is executable within the award period. It should connect aims, milestones, personnel, dependencies, deliverables, and decision points. + +## Timeline Elements + +- **Aims and tasks**: Break each aim into concrete work packages. +- **Milestones**: Define measurable completion points, not just activities. +- **Dependencies**: Identify tasks that require prior data, approvals, hires, or equipment. +- **Decision points**: Specify go/no-go thresholds and alternatives. +- **Deliverables**: Publications, datasets, software, prototypes, reports, or demonstrations. +- **Compliance gates**: IRB, IACUC, data-use agreements, safety reviews, and export controls. + +## Planning Pattern + +1. List all aims and sub-aims. +2. Assign each task to a quarter or project period. +3. Add hiring, procurement, regulatory, and setup lead times. +4. Mark dependencies between tasks. +5. Define success metrics for each milestone. +6. Add contingency paths for high-risk tasks. + +## Agency Emphasis + +- **NSF**: Integrate research, education, broader impacts, evaluation, and dissemination. +- **NIH**: Show feasibility for enrollment, experiments, analysis, rigor, and data sharing. +- **DOE**: Align tasks with program deliverables, user facilities, and reporting periods. +- **DARPA**: Use aggressive but credible phases with quantitative milestones and demos. + +## Common Pitfalls + +- Treating the timeline as a decorative Gantt chart rather than an execution plan. +- Scheduling major approvals after dependent work begins. +- Omitting time for hiring, onboarding, equipment procurement, or data-use agreements. +- Making all aims run sequentially when parallel work is possible. +- Failing to define what happens if a milestone is missed. -- 2.54.0 From c11aca9c7feda6a61313fabeebb41bbbeca2bef5 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:48:42 +0000 Subject: [PATCH 8/9] [upstream-sync] skills/onekgpd/SKILL.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../catalogue/skills/onekgpd/SKILL.md | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/SKILL.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/SKILL.md index 1b8d22ed..be1aa561 100644 --- a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/SKILL.md +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/SKILL.md @@ -1,8 +1,8 @@ --- lineage_type: import -upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/0807ddbc/skills/onekgpd/SKILL.md -upstream_sha: 0807ddbc -imported_at: 2026-06-30 +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/skills/onekgpd/SKILL.md +upstream_sha: 708d419d +imported_at: 2026-07-13 prompt_class: unknown upstream_changes: accepted name: onekgpd @@ -17,9 +17,9 @@ description: > Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations. license: MIT -compatibility: Requires Python >=3.12. Variant and sample queries require outbound network access to the public 1000 Genomes query endpoint over TLS; the sample/population metadata commands run fully offline over a data file bundled in the skill. No credentials, API keys, or environment variables are used. +compatibility: Requires Python >=3.11. Variant and sample queries require outbound network access to the public 1000 Genomes query endpoint over TLS; the sample/population metadata commands run fully offline over a data file bundled in the skill. No credentials, API keys, or environment variables are used. allowed-tools: Write Bash -metadata: {"version": "1.0", "skill-author": "Dnaerys"} +metadata: {"version": "1.2", "skill-author": "Dnaerys"} --- # OneKGPd: Individual-Level Queries over the 1000 Genomes Project @@ -189,6 +189,9 @@ filtering is not necessarily echoed back on the returned variant. > `--gnomad-exomes-af-gt 0` selects variants that *are* in gnomAD exomes; a > returned `gnomad_exomes_af` of `0.0` means the variant is absent from gnomAD > exomes. The same convention for gnomAD genomes AF. +> Conversely, `--gnomad-exomes-af-lt` / `--gnomad-genomes-af-lt` bounds **include** +unannotated variants: "AF < X in gnomAD" includes variants with gnomAD AF = 0, +i.e. unannotated; pair it with `--gnomad-*-af-gt 0` to require presence in gnomAD. > [!NOTE] > `am_score` of `0.0` means not scored or not annotated by AlphaMissense - it does not mean `benign`. @@ -236,7 +239,7 @@ The full per-flag tables live in - `count-variants` — count variants in a region, cohort-wide. - `select-variants` — select variants in a region, cohort-wide. Use `--limit N` - (hard cap, default 1000) **or** `--page-size N` (retrieve the full set in + (hard cap, default 200) **or** `--page-size N` (retrieve the full set in pages); the two are mutually exclusive. The summary flags `truncated` when the cap is reached. - `count-variants-in-samples` — as `count-variants`, restricted to @@ -244,9 +247,11 @@ The full per-flag tables live in - `select-variants-in-samples` — as `select-variants`, restricted to `--samples NAME1,NAME2,...` (required). -Each returned variant carries these 19 keys: `chr`, `start`, `end`, `ref`, -`alt`, `af`, `ac`, `an`, `homc`, `hetc`, `misc`, `homfc`, `hetfc`, `misfc`, -`gnomad_exomes_af`, `gnomad_genomes_af`, `am_score`, `amino_acids`, `biallelic`. +Each returned variant carries these 22 keys: `chr`, `start`, `end`, `ref`, +`alt`, `af`, `ac`, `an`, `hom_samples`, `het_samples`, `mis_samples`, +`hom_samples_fx`, `het_samples_fx`, `mis_samples_fx`, `hom_samples_mxy`, +`het_samples_mxy`, `mis_samples_mxy`, `gnomad_exomes_af`, `gnomad_genomes_af`, +`am_score`, `amino_acids`, `biallelic`. ClinVar significance and VEP consequence are filter criteria only and are not returned. Full schema: [references/onekgpd_commands.md](references/onekgpd_commands.md). -- 2.54.0 From 62e38336f06a58b4dcb6e6958ecb6a7e9a4cef5d Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 13 Jul 2026 20:48:57 +0000 Subject: [PATCH 9/9] [upstream-sync] skills/onekgpd/references/onekgpd_commands.md from K-Dense-AI/scientific-agent-skills@708d419d [unknown] --- .../onekgpd/references/onekgpd_commands.md | 31 ++++++++++++------- 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/references/onekgpd_commands.md b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/references/onekgpd_commands.md index 12a2e1e5..c54eb28e 100644 --- a/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/references/onekgpd_commands.md +++ b/upstream/K-Dense-AI-scientific-agent-skills/catalogue/skills/onekgpd/references/onekgpd_commands.md @@ -2,9 +2,9 @@ title: "OneKGPd command reference" task: "" lineage_type: import -upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/0807ddbc/skills/onekgpd/references/onekgpd_commands.md -upstream_sha: 0807ddbc -imported_at: 2026-06-30 +upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/708d419d/skills/onekgpd/references/onekgpd_commands.md +upstream_sha: 708d419d +imported_at: 2026-07-13 prompt_class: unknown upstream_changes: accepted author: upstream @@ -84,6 +84,10 @@ Mutual exclusions enforced: `--biallelic-only`/`--multiallelic-only`, AlphaMissense score bounds. Setting a `*-gt` ≥ its matching `*-lt` defines an empty range and returns nothing. +The `--gnomad-exomes-af-lt` / `--gnomad-genomes-af-lt` bounds **include** unannotated +variants: "AF < X in gnomAD" includes variants with gnomAD AF = 0, i.e. unannotated; +pair it with `--gnomad-*-af-gt 0` to require presence in gnomAD. + --- ## Commands @@ -196,19 +200,22 @@ and VEP consequence are **not** echoed back on a returned variant): | `end` | int | 1-based inclusive end. | | `ref` | str | Reference allele. | | `alt` | str | Alternate allele. | -| `af` | float | 1000 Genomes dataset allele frequency. | -| `ac` | float | Dataset allele count (0.5 for male non-PAR het calls on sex chromosomes). | +| `af` | float | Dataset allele frequency. | +| `ac` | float | Dataset allele count (0.5 for male non-PAR het calls on on X and Y chromosomes). | | `an` | int | Dataset allele number. | -| `homc` | int | Homozygous allele count. | -| `hetc` | int | Heterozygous allele count. | -| `misc` | int | Missing (no-call) allele count. | -| `homfc` | int | Female homozygous count (sex chromosomes). | -| `hetfc` | int | Female heterozygous count (sex chromosomes). | -| `misfc` | int | Female missing count (sex chromosomes). | +| `hom_samples` | int | Number of all samples with a homozygous genotype. | +| `het_samples` | int | Number of all samples with a heterozygous genotype. | +| `mis_samples` | int | Number of all samples with a missing (no-call) genotype. | +| `hom_samples_fx` | int | Number of female samples with a homozygous genotype, X chromosome only (0 outside X). | +| `het_samples_fx` | int | Number of female samples with a heterozygous genotype, X chromosome only (0 outside X). | +| `mis_samples_fx` | int | Number of female samples with a missing (no-call) genotype, X chromosome only (0 outside X). | +| `hom_samples_mxy` | int | Number of male samples with a homozygous genotype, X & Y chromosomes only (0 outside X and Y). | +| `het_samples_mxy` | int | Number of male samples with a heterozygous genotype, X & Y chromosomes only (0 outside X and Y). | +| `mis_samples_mxy` | int | Number of male samples with a missing (no-call) genotype, X & Y chromosomes only (0 outside X and Y). | | `gnomad_exomes_af` | float | gnomAD v4.1 exomes AF. `0.0` = absent from gnomAD exomes. | | `gnomad_genomes_af` | float | gnomAD v4.1 genomes AF. `0.0` = absent from gnomAD genomes. | | `am_score` | float | AlphaMissense score. `0.0` = not annotated. | -| `amino_acids` | str | Amino-acid substitution (HGVSp / VEP `Amino_acids`). | +| `amino_acids` | str | HGVSp Amino-acid substitution. | | `biallelic` | bool | Whether the site was biallelic in the input VCFs. | --- -- 2.54.0