To identify genome wide variants, sequences of each species were trimmed using Flexbar [ 25] and were aligned to the reference assembly from which they were derived using BWA-mem [ 26].
Twain broke with the tradition of asking "Who Am I?" and its species-wide variant "Who Is Man?" on the grounds that a "who-question" is a leading question.
Tools for genome-wide variant identification can be grouped into four categories: (i) germline callers, (ii) somatic callers, (iii) CNV identification and (iv) SV identification.
The same massively parallel sequencers are simultaneously being used for whole-genome resequencing and comprehensive, genome-wide variant discovery in studies of somatic diseases such as cancer.
The germline mutation rate was extrapolated from the frequency of experimentally validated germline mutations relative to the total number of potential germline mutations from the genome-wide variant calls.
Figure 8 shows that breakpoint intervals were significantly longer than the average spacing between variants (median 106 bp, compared with 15 bp for genome-wide variant spacing; K-S test: D = 0.50, p-value << 0.001).
NGS technologies offer the advantage of unbiased genome-wide variant detection in small nuclear families and sporadic cases that previously could not be used effectively with traditional linkage analysis.
We used three publicly available resources to extract genome-wide variant frequency data: the Exome Sequencing Project (ESP6500) (60), the 1000 Genomes Project (Oct 2014) (61) and the ExAC (62).
In order to assess the extent of variability that the KWP1 genome exhibits, we performed inter-genome comparisons with 10 representative genomes from four continents and derived nearest-neighbor tree based on genome-wide variant positions shared among genomes.
Other studies can only avail themselves to small, underpowered pedigrees for linkage, however, there is no longer a requirement for a priori statistically significant linkage, since WES and WGS are genome-wide variant identification methods, with no additional costs involved to examine further regions in the genome.
