Allele Balance Ratio
The Allele Balance Ratio is another filter that you can use to determine if an allele is a true allele or a false positive. The Allele Balance ratio is defined as the maximum value for one of the following:
• Allele Forward %/Total Forward % or Total Forward %/Allele Forward %
• Allele Reverse %/Total Reverse % or Total Reverse %/Allele Reverse %
with different default thresholds specified for SNPs (2.5) and indels (5.0).
Consider the following scenario, where:
• Two forward reads and 79 reverse reads with the allele (a SNP), for 81 total allele reads.
• 1758 total forward reads and 6055 total reverse reads, for 7812 total reads.
This results in the following:
Value | Calculation |
|---|---|
Total Forward % | 1758/7813 = 0.22501 |
Total Reverse % | 6055/7813 = 0.77499 |
Allele Forward % | 2/81 = 0.02469 |
Allele Reverse % | 79/81 = 0.97531 |
Allele Forward %/Total Forward % | 0.02469/0.22501 = 0.9113 |
Total Forward %/Allele Forward % | 0.22501/0.02469 = 9.1134 |
Allele Reverse %/Total Reverse % | 0.97531/0.77499 = 1.2585 |
Total Reverse %/Allele Reverse % | 0.77499/0.97531 = 0.7946 |
Determination: Because 9.1134 is > 2.5, this allele is filtered from the results. | |
 | If an allele is determined to be one directional, then an Allele Balance Ratio is not calculated. Instead, if the allele is a major allele, then it is not filtered from the results. |
Although SoftGenetics has supplied the default values for the calculation of the Allele Balance Ratio, you can always edit one or both of these thresholds. If you edit a value, you must try to maintain a balance of sensitivity versus specificity. For example, if you are concerned that variants are being called that are actually false positives and the variants also appear to be unbalanced, then you might tighten the restrictions on variant calling and decrease the applicable threshold value. Conversely, if some expected variants are not being called, then you might loosen the restrictions on variant calling and increase the applicable threshold value.