snp2hgvs

name	snp2hgvs
description	Use when converting NCBI dbSNP docsum XML into HGVS-oriented XML records for downstream variant normalization or annotation pipelines.
disable-model-invocation	true
user-invocable	true

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

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.