How do I install the Snp2hgvs skill?

Run npx skillmds add vimalinx/snp2hgvs in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Snp2hgvs free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Snp2hgvs?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Snp2hgvs by vimalinx — Agent Skill

Name: Snp2hgvs
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

snp2hgvs

Small bash wrapper over xtract and transmute. It reads dbSNP DocumentSummarySet XML, selects matching DocumentSummary records, and emits structured HGVS XML with one or more <Variant> blocks per rsID.

Quick Start

Command: efetch -db snp -id <rsid> -format docsum | snp2hgvs
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/snp2hgvs
Expected input: dbSNP docsum XML from Entrez Direct

When To Use This Tool

Converting dbSNP docsum XML into HGVS-centered XML for one or more rsIDs
Bridging from efetch -db snp -format docsum into later HGVS/SPDI conversion steps
Extracting multiple genomic, coding, or protein HGVS representations from the same SNP record
Feeding rsID-derived HGVS records into hgvs2spdi, spdi2prod, or custom XML processing

Common Patterns

# Convert one rsID into HGVS XML
efetch -db snp -id 104894914 -format docsum | snp2hgvs

# Convert multiple dbSNP docsum records, then continue into SPDI
efetch -db snp -id 104894914,104894915 -format docsum | snp2hgvs | hgvs2spdi

# Full chain hinted by the wrapper source
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2prod

Recommended Workflow

Fetch SNP records from Entrez Direct in -format docsum, not an unrelated XML flavor.
Pipe the docsum XML directly into snp2hgvs.
Inspect the resulting <HGVS> document if you care about class/type distinctions across genomic, coding, or protein variants.
Chain into hgvs2spdi or other downstream normalizers only after confirming the wrapper emitted the variant forms you need.

Guardrails

There is no safe standalone help/version path: both -h and --version fell through to xtract and failed with No data supplied to xtract from stdin or file.
The wrapper depends on both xtract and transmute being available on PATH.
Source inspection shows it expects DocumentSummarySet / DocumentSummary XML with SNP_ID; it is not a generic rsID-to-HGVS web client.
In live testing on rs104894914, the wrapper emitted <HGVS> XML containing multiple <Variant> records, including genomic (NC_000023.11:g.154191716T>C) and coding (NM_000513.2:c.607T>C) forms.

---name: snp2hgvsdescription: Use when converting NCBI dbSNP docsum XML into HGVS-oriented XML records for downstream variant normalization or annotation pipelines.--- # snp2hgvs Small bash wrapper over `xtract` and `transmute`. It reads dbSNP `DocumentSummarySet` XML, selects matching `DocumentSummary` records, and emits structured HGVS XML with one or more `<Variant>` blocks per rsID. ## Quick Start - **Command:** `efetch -db snp -id <rsid> -format docsum | snp2hgvs` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/snp2hgvs` - **Expected input:** dbSNP docsum XML from Entrez Direct ## When To Use This Tool - Converting dbSNP docsum XML into HGVS-centered XML for one or more rsIDs - Bridging from `efetch -db snp -format docsum` into later HGVS/SPDI conversion steps - Extracting multiple genomic, coding, or protein HGVS representations from the same SNP record - Feeding rsID-derived HGVS records into `hgvs2spdi`, `spdi2prod`, or custom XML processing ## Common Patterns ```bash # Convert one rsID into HGVS XML efetch -db snp -id 104894914 -format docsum | snp2hgvs ``` ```bash # Convert multiple dbSNP docsum records, then continue into SPDI efetch -db snp -id 104894914,104894915 -format docsum | snp2hgvs | hgvs2spdi ``` ```bash # Full chain hinted by the wrapper source efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2prod ``` ## Recommended Workflow 1. Fetch SNP records from Entrez Direct in `-format docsum`, not an unrelated XML flavor. 2. Pipe the docsum XML directly into `snp2hgvs`. 3. Inspect the resulting `<HGVS>` document if you care about class/type distinctions across genomic, coding, or protein variants. 4. Chain into `hgvs2spdi` or other downstream normalizers only after confirming the wrapper emitted the variant forms you need. ## Guardrails - There is no safe standalone help/version path: both `-h` and `--version` fell through to `xtract` and failed with `No data supplied to xtract from stdin or file`. - The wrapper depends on both `xtract` and `transmute` being available on `PATH`. - Source inspection shows it expects `DocumentSummarySet` / `DocumentSummary` XML with `SNP_ID`; it is not a generic rsID-to-HGVS web client. - In live testing on rs104894914, the wrapper emitted `<HGVS>` XML containing multiple `<Variant>` records, including genomic (`NC_000023.11:g.154191716T>C`) and coding (`NM_000513.2:c.607T>C`) forms.

Frequently asked questions