/** Value used for filtering tumor variants. If a position that has been found to have a variant in tumor, has reads with the variant alternate allele also in the normal sample and if the number of such reads is higher than the value given with this parameter and the sum of the quality scores in these reads in this position is higher than given with the parameter 'maxAltAllelesInNormalQScoreSum', then the variant is filtered out from the final result.
/** Value used for filtering tumor variants. If a position that has been found to have a variant in tumor, has reads with the variant alternate allele also in the normal sample and if the fraction of such reads from all reads is higher than the value given with this parameter and the sum of the quality scores in these reads in this position is higher than given with the parameter 'maxAltAllelesInNormalQScoreSum', then the variant is filtered out from the final result.
/** Value used for filtering tumor variants to exclude false positives caused by misalignments evidenced by alternate alleles occurring near the start and end of reads. Variants are rejected if their median distance from the start/end of of the reads is lower than this parameter and if the median absolute deviation is lower than the value given with the parameter 'pir_mad_threshold'. Filtering is done only if the parameter 'enableClusteredReadPositionFilter' is set to true.
/** Value used for filtering tumor variants to exclude false positives caused by misalignments evidenced by alternate alleles occurring near the start and end of reads. Variants are rejected if their median distance from the start/end of the reads is lower than given with the parameter 'pirMedianThreshold' and if the median absolute deviation is lower than given with this parameter. Filtering is done only if the parameter 'enableClusteredReadPositionFilter' is set to true.
/** If this parameter is set to true, then tumor variants are filtered to exclude false positives that are caused by misalignments evidenced by alternate alleles occurring near the start and end of reads. For filtering values of the parameters 'pirMedianThreshold' and 'pirMadThreshold' are used.