Calculate allele frequencies at each locus in each populationRland
By default, the minimum allele frequency of the non-reference allele is 2, but it can be changed with option-mto analyse other slices of RAS. The--ascertainInoption can be used to define the comma-separated set of populations that should be used for rare allele ascertainment. By default, ...
Results Definitions and premises. • The frequency of a risk allele in a general population: p. • The frequency of non-risk allele in a general population: q. • The frequency of a risk allele in patients: u. • The frequency of non-risk allele in patients: v. • The ...
Results Definitions and premises. • The frequency of a risk allele in a general population: p. • The frequency of non-risk allele in a general population: q. • The frequency of a risk allele in patients: u. • The frequency of non-risk allele in pat...
{0.05,0.01,0.005,0.001,0.0005} Minor allele frequency (MAF) threshold. --binarity {binary,countvariants}, -b {binary,countvariants} Count the number of individuals (binary), or the total number of variants seen in individuals (countvariants). The latter option will count an individual multiple...
Arrays.fill(indexOfOriginalAlleleForNewAllele, -1);// note that we don't care about the reference allele at position 0for(intnewI =1; newI < newAlleles.size(); newI++) {finalAllele newAlt = newAlleles.get(newI);for(intoldI =0; oldI < numOriginalAlleles -1; ...
Calculate allele numbers (frequency in the statistical sense) at each locus in each populationRland