Sentence examples for mapping quality threshold from inspiring English sources
We use mapping quality threshold 1 for MAQ and 10 for BWA to determine confident mappings.
Mapped reads of each strain were filtered using a mapping quality threshold of 30 using SAMtools v1.1 [ 63].
Alignment files were further filtered for mapping quality (threshold 75), number of mismatches to the reference ('ΝΜ' threshold 10) and for proper pair mapping with BamTools [ 71].
Variants and genotypes were called using the HaplotypeCaller tool from the GATK (v2.7-2) (McKetnalet al. 2010) with a minimum mapping quality threshold of 25.
A low mapping quality threshold setting leads to many candidate genes for further experimental validation, but can also introduce false positive discoveries.
Furthermore, the output of NextGenMap+MaxSSmap reveals many high scoring alignments well above the mapping quality threshold that warrant further study.
Furthermore, when used with stringent mapping quality thresholds, the SNVMix2 model can effectively use the base qualities by probabilistic weighting to confer higher accuracy.
A script to choose optimal base and mapping quality thresholds, given ground truth [or orthogonal single nucleotide polymorphism (SNP) array] data, is provided in the software package.
Table 2 shows the sensitivity, precision and F-measure results of SNVMix2, SNVMix1 and SNVMix2 combined with base and mapping quality thresholding at both 10× and 40× coverage at a p SNV) (Section 2) threshold determined using a FPR ≤ 0.01.
We therefore only retained elements for which >80% of all informative sites met the strict read depth and mapping quality constraints imposed by the 1000 Genomes Consortium (Altshuler et al. 2012) for population genetic analyses using these data (see Methods); these criteria enforce both strict minimum and maximum read depth as well as minimum mapping quality thresholds.
True positive (TP) observed calls matched the reference call in position, genotype and alternate bases, and were based on those variants that are callable (that is, the proportion of variants that are detected at or above the predefined alignment, mapping quality and variant calling quality thresholds).
