Allele Score Difference
In GeneMarkerHTS, a quality score is calculated for every SNP or insertion allele as the median of the base Phred quality score from the original data. Because base quality scores are not possible for a deletion, the quality scores for the bases that surround a deletion are used instead. The Allele Score Difference filter, which is based on the base quality score for an allele, is applied individually for each direction as follows:
• The total number of reads for the minor allele is recorded.
• The base quality score for each minor allele is subtracted from the base quality score for the major allele to calculate the Allele Score Difference.
If the both of the following criteria are met, then the variant is assumed to be a false positive and the minor allele is filtered from the alignment results:
• The Allele Score Difference is greater than its set threshold.
• The total number of reads for the minor allele is greater than or equal to five.
If either of these criteria are not met, then the allele is assumed to be a true allele and it is not filtered from the results.