This tool can infer the numbers of crossovers or breakpoints based on SNP markers. The tool was tested on 50K barley and 25K wheat SNPs arrays however it is not limited to these.

This tool is a thick client which means computation is done on your edge (ie. on the device you accessing the site).

It takes two input files. Input 1 is the HAPMAP file for the parents if you have that. Only the first two sample columns of the HAPMAP will be used as parent 1 and 2.

A template of HAPMAP can be downloaded here for convenience.

Columns descriptions for HAPMAP:

• rs#: SNP identifier (required)
• alleles: SNP alleles per dbSNP
• chrom: Chromosome mapping (required)
• pos: SNP position on chromosome (required)
• strand: Orientation on DNA strand (+/-)
• assembly#: Reference sequence version
• center: Genotyping center name
• protLSID: HapMap protocol identifier
• assayLSID: Identifier for assay used
• panelLSID: Identifier for genotyped panel
• QCcode: Quality control flag
• sample1: Sample name (required)

By pressing process the calculation starts. First inputs are validated, then crossover events by chromosomes and lines are estimated. A summary report is provided at the end and results will be available to download.