What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually means?
This refers to haplotype phase (aka gametic phase). This essentially means knowing which allele belongs to which copy of the chromosome, or alternatively, which alleles appear together on the same chromosome.
In short-read sequencing, for example, it is difficult to resolve the haplotype of two heterozygous SNPs if they have not been covered by the same read. If you observe A/a and B/b, you do not know whether you have AB + ab or aB + Ab. So you would say you do not know the phasing.
See the Wikipedia links for more information.
phasing is the relationship between adjacent alleles on the same chromosome i.e. if they are in cis or trans configuration. In other words, weather two alleles are indeed on the same chromosome or on different chromosome. One of the reason alleles get shuffled is by process called recombination where chromosome exchange happens. Majority of current methods infer the phase using linkage disequilibrium principle however with advent of whole chromosome sequencing it's possible to determine empirically the phase from related samples. i.e. father, mother, son