File contains one line for each crossover observed. Ordered by chromosome, then crossover start position, then donor, then cell. Positions are in hg38 coordinates.
Note: individual crossovers are not validated; visualize or otherwise interrogate any specific crossover of interest.
Per above, Crossover calling is sensitive to artifacts of SNP calling. For example, unknown paralogs in the genome result in many SNPs being called in close proximity to one another, sometimes biased toward one haplotype. This can result in stretches of crossovers that originate from the same haplotype. (These can be identified by scanning for windows where the same 'from.haplotype' is shared by 25 crossovers in a row - or by 23 out of 25 crossovers in a window. Only 0.17% of all crossovers fall into these windows, 0-0.93% of each sperm donor's crossovers.) We thank eagle-eyed users of this data (Russ!) for noting these same-haplotype-biased crossover windows. Depending on the sensitivity of your analysis of interest, you may wish to remove these crossovers, as many in each window do not reflect biological recombination events.
Column descriptions:
donor: sperm donor
cell: cell barcode
chr: chromosome
pos.leftbound: position of left boundary of crossover (hg38)
pos.rightbound: position of right boundary of crossover (hg38)
snpindex.leftbound: SNP index (count, 1-based) at left boundary of crossover
snpindex.rightbound: SNP index (count, 1-based) at right boundary of crossover
nsnps.onchrincell: Total number of SNPs on chromosome in this cell (for interpreting SNP index boundaries)
from.haplotype: Haplotype before the crossover
to.haplotype: Haplotype after the crossover