MVEL Script Restriction: Example Cases | International Cancer Genome Consortium
What does this script restriction for the "mutated_to_allele" field in the Simple Somatic Mutations Primary (ssm_p) file mean?
var allele = null;
if (ctrlAlleles contains mutated_to_allele) {
for (allele:tumourAlleles) {
if (mutated_to_allele != allele) {
return false
}
}
} else {
if (!(tumourAlleles contains mutated_to_allele)) {
return false
}
}
This MVEL script restriction checks to make sure "mutated_to_allele" is one of the mutated alleles in tumour_genotype. The following example mutation is not valid:
Invalid Mutation:
reference_genome_allele: G
control_genotype: G/G
tumour_genotype: G/T
mutated_from_allele: G
mutated_to_allele: G
One of the alleles in tumour_genotype is actually mutated (G/T). Therefore, mutated_to_allele should be "T" instead of "G".
Valid mutation:
reference_genome_allele: G
control_genotype: G/G
tumour_genotype: G/T
mutated_from_allele: G
mutated_to_allele: T