find_primer_snps
Read-only
Find known SNPs under primers, the check NCBI Primer-BLAST makes with "Primer binding site may not contain known SNP".
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pairs | No | the pairs to check, as design_primer_pairs' `pairs` output (each with forward and reverse start/end on the template). | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| forward | No | a forward primer to locate on the template by exact match, when no `pairs` are given. | |
| reverse | No | a reverse primer to locate by exact match of its reverse complement. | |
| snp_set | No | `dbSnp155Common`: About 15 million variants with a minor allele frequency of at least 1% in 1000 Genomes Phase 3. The default. `dbSnp155`: Every mapped variant: 1.06 billion locations on hg38, so few primers avoid them all. `dbSnp155ClinVar`: About 820,000 variants ClinVar mentions, benign and pathogenic alike. | dbSnp155Common |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| assembly | Yes | the UCSC assembly id the template was cut from (hg38, mm39, danRer11…). | |
| position | Yes | where the template sits in that assembly, as chromosome:position, 1-based: the lowest assembly coordinate the template covers. The check finds which strand the template reads on itself. | |
| template | No | the sequence the primers sit on. Left empty, the open record is used. | |
| window_end | No | 1-based last base of the span to check. Advanced. | |
| window_start | No | 1-based first base of the template span to check. Unset = the whole template. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| snps | Yes | every SNP in the span, placed on the template (0-based, end-exclusive), with alleles as they read on the template's strand and whether the template spells dbSNP's reference allele there | |
| flagged | Yes | how many primers sit on at least one known SNP | |
| primers | Yes | every primer checked: its name, span on the template, strand, and the SNPs under it with rsID, alleles, minor allele frequency and distance from the 3′ end (1 = the 3′ base) | |
| excluded | Yes | the SNP spans, for design_primer_pairs' `excluded` |