Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server

Variant File Format

The input requirements are solely a list of variants including the chromosome, start position, end position, and reference and variant alleles - transferred via a network connection for automated processing or provided via a local file.

One of a few standard file formats, including:


SG ADVISER uses hg19 as a reference genome. Loading variants with hg18 coordinates will result in an error. If you have any hg18 variants that you want to annotate we recommend you use liftOver ( Batch Coordinate Conversion tool available at UCSC) to convert the variants. You can use the online version of the tool, or download liftOver and run it locally.

Most web-based interfaces (ex. UCSC genome browser) report physical positions in 1-based coordinates, please make sure you insert variants with 0-based coordinates.

In all cases files are processed and converted to an internal 8 column tab-delimited format.

Example Input:

1. Haplotype number, maternal or paternal inheritance, line number or placehoders ("-" or "*") are acceptable.
2. Chromosome (with syntax: `chr1`, `chr22`, `chrX`, etc.)
Unsupported chromosomes: chrM, chrUn (unmapped), chr7_xyz (alternate haplotype)
3. Start position (0-based coordinates)
4. End position (0-based coordinates)
5. Variant type (`snp`, `ins`, `del`, `delins`)
start position end position
snp start start + 1
ins start start
del start start + length(ref allele)
delins start start + length(ref allele)
6. Reference allele(s) (A,C,T,G,-)
Explicitly provide `-` for insertions
The unknown base `N` is disallowed
7. Observed allele(s) (A,C,T,G,-)
Explicitly provide `-` for deletions
The unknown base `N` is disallowed
8. Notes. Arbitrary string data containing no tab characters

Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server