BYSTRO AI

Query Variant Coordinates

Search for variants by genomic position using chromosome and coordinate information. Bystro supports multiple coordinate formats and range queries for flexible genomic searches.

Method 1: Field-Based Search

Search using the chrom andpos fields separately. This method gives you precise control over each component of the genomic coordinate.

Field Format Guidelines

  • ▶chrom field uses UCSC conventions (e.g., chr1, chr2, chrX, chrY)
  • ▶pos accepts scientific notation (1e3), decimal (1000), or comma-separated (1,000)
  • ▶Syntax: fieldname:value (e.g., chrom:chr1 pos:2e7)

Let's search for chrom:chr19 pos:44908822, which contains one of the diagnostic Alzheimer's disease-associated APOE mutations:

Image showing how to search using chrom and pos fields

Searching for APOE variant using separate chrom and pos fields

Method 2: Coordinate Format Search

Use the familiar chrN:position format for quick coordinate searches. This automatically searches both the chrom and pos fields.

Accepted Formats

  • • chr17:41,215,920 (with commas)
  • • chr17:41215920 (without commas)
  • • chr17:4.12e7 (scientific notation)

Benefits

  • • Familiar genomics format
  • • Faster for single position queries
  • • Compatible with genome browsers
Animation showing how to search using chrN:pos format

Same APOE search using the convenient chr19:position format

Position Range Queries

Search genomic regions using range syntax to find all variants within a specific interval. This is particularly useful for analyzing genes, regulatory regions, or chromosomal segments.

Range Query Syntax

Recommended Format:

  • • pos:[start TO end]
  • • Brackets are optional but safer for complex queries
  • • TO keyword is explicit and clear

Alternative Formats:

  • • pos1 - pos2 (dash separator)
  • • pos1 ... pos2 (ellipsis separator)

Range Query Caution

Be careful with the dash (-) operator as it has multiple meanings:

  • • Numeric sign: -100 (negative number)
  • • Exclusion operator: -termToExclude (exclude results containing this term)
  • • Range separator: pos1 - pos2 (position range)

Use TO syntax for clarity in complex queries.

Example: 3q29 Microdeletion Region

Let's search the 1.6Mb 3q29 region associated with microdeletion syndrome using chr3:195.7e6 - 197.4e6:

Animation showing how to search position ranges

Searching the 3q29 microdeletion region (chr3:195.7M-197.4M) to find all variants in this clinically relevant interval

Practical Applications

Single Variant Lookup

Find specific known variants by exact coordinates

chr17:41215920

Gene Region Analysis

Search entire genes or regulatory regions

chrom:chr17 pos:[41.1e6 TO 41.3e6]

Chromosomal Segments

Analyze large genomic regions or cytogenetic bands

chr3:195e6 - 200e6

Coordinate Search Tips

• Combine with filters: Use coordinate searches with functional annotations for targeted analysis

• Scientific notation: Use 1e6 for millions, 1e3 for thousands to avoid typing errors

• Check genome build: Ensure your coordinates match the reference genome used in your dataset

• Range queries: Consider using gene names for known genes rather than manual coordinate ranges

Performance Note

Dataset used in examples: 1000 Genomes Project (73,452,337 variants in 27,192 genes, queries typically complete in ~0.5 seconds)