Variant File Format
The input requirements are solely a list of variants including the chromosome, start position(0-based coordinates), end position(0-based coordinates), 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:
- CNVnator. Example of CNVnator input file can be found here.
- Complete Genomics Master Variations (cnvSegmentsDiploidBeta-[ASM-ID].tsv) Example of Complete Genomics file can be found here.
- 5 column tab delimited BED-like file format are accepted Example of BED file can be found here.
Example Input:
| 1. | Chromosome (with syntax: `chr1`, `chr22`, `chrX`, etc.) |
| Unsupported chromosomes: chrM, chrUn (unmapped), chr7_xyz (alternate haplotype) | |
| 2. | Start position (0-based coordinates) |
| 3. | End position (0-based coordinates) |
| 4. | Variant type ('gain' or 'loss') |
| 5. | Notes. Arbitrary string data containing no tab characters |