Sentence examples for using the genome option from inspiring English sources
(2) PLINK is a popular tool for running association studies and many users generate a file containing IBD probabilities and IBS counts using the, genome option.
A heuristic search using the Genome BLAST (blastn) option was performed using default parameters.
Structural rearrangements between the two genomes were detected using the "nucmer" program within the MUMmer package (Delcher et al. 2002; default parameters except –maxmatch option) and visualized using the Genome Synteny Viewer (Revanna et al. 2011).
The two sequenced genomes were aligned using the genome alignment software progressiveMauve [ 66], using default options.
CADD has no alterable parameters; however, FunSeq was run using the 'personal genome' option and a MAF cutoff of 0.1.
In the merged dataset, pairwise identity-by-state (IBS) relations were calculated for each pair of individuals (representing the average proportion of alleles shared by those individuals) using PLINK (–genome option).
Relatedness among subjects was checked using PLINK –genome option.
To identify potential lateral genetic transfers from Wolbachia to the host nuclear genome, the nuclear genome was queried against the 921-kbp wDi genome using the dc-megablast option in BLASTN (NCBI-blast+2.2.25) with default settings.
Comparable data were not available for dog, sheep, and pig so we launched RepeatMasker on the whole dog (CanFam 2.0 May 2006), sheep (Oarv2.0 March 2011), and pig (Sscrofa9 April 2009) genome assemblies using the slow option.
For the prairie vole-rat comparison in which the orthologous positions of the mapped prairie vole BAC clones in the rat genome were indirectly inferred via their orthologous location in the mouse genome using the UCSC Genome Browser 'convert' option [ 19], the GRIMM algorithm estimated a total of 37 rearrangements (3 inversions and 34 interchromosomal) between the prairie vole and rat.
The find_related_samples module uses PLINK's genome option to estimate the relatedness of study participants using identity-by-descent and identity-by-state for each sample pairs.
