A common method of minimizing errors in large DNA sequence data sets is to drop variable sites with a minor allele frequency (MAF) below some specified threshold. Although widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little...
The next quality control step is to discard SNPs with a lowminor allele frequency(MAF) as they increase the probability of detecting association when there is none (spurious association). The threshold often used is to exclude SNPs with a MAF below0.05. This can be performed using the “--...
The threshold of base QV also has a minor impact on the accuracy. A non-zero threshold increases the accuracy on the Bordetella spp. data (Fig. 4a), but decreases the accuracy on the E. coli data (Fig. 4b). This might be because masking bases with low QV removes some sequencing ...
#' threshold macTh and ii) p_markerQC, a ggplot2-object 'containing' a #' sub-paneled plot with the QC-plots of \code{\link{check_snp_missingness}}, #' \code{\link{check_hwe}} and \code{\link{check_maf}}, which can #' be shown by print(p_markerQC). #' List entries conta...
The functional avidity can also impact CD8+ T cell activation since it is considered as a quantitative determinant of the activation threshold of a T-cell clone [56,57]. Hence, differentiation and expansion protocols used for stimulating a memory repertoire might need to be optimized depending on...
However, in the regions studied, the 0.05 cutoff threshold did not significantly increase power above the 0.10 threshold (P = 0.191 in Han; 1.000 in Tibetans), and did not improve resolution over the 0.10 value for population- specific haplotypes (P = 0.592) neither. Furthermore the 0.05 ...
Here we analyze samples from both laboratory-defined mixtures and complex multi-contributor touch samples using a single nucleotide polymorphism (SNP) panel comprised of 2311 low-minor-allele-frequency loci, combined with massively parallel sequencing (MPS). This approach demonstrates that as many as ...