Sentence examples for threshold of variant from inspiring English sources

Next, we computed the precision and the sensitivity (i.e. recall) at each threshold of variant quality and SVM score, respectively, and plotted precision by sensitivity.

If we require ≥ 4 reads per variant while keeping the threshold of minor variant abundance at ≥ 10%, the correct predictions rise to 75% (9/12).

When considering AS according to 454 reads alone, 64% (80/125) of the well-supported cases of AS are predicted correctly, which increases to 79% (30/38) if we require ≥ 4 reads per variant while keeping the threshold of minor variant abundance at ≥ 10%.

The results were used as input for the Bioconductor [ 44] Rsamtools version 1.6.0 package to obtain the possible nucleotide variants with a cut-off coverage of 4x, a threshold of 2 variants in the position and a base call quality cut-off of the PHRED score Q20 on average, where Q = -10 log10P, and the score stands for the probability of a wrong base being called.

From these data it will also be possible to estimate whether a liability threshold of common variants is sufficient to cause schizophrenia, and whether this can be applied to individual risk prediction.

According to DVs, components are divided into three types of modules based on two thresholds of the variant.

SIFT assigns a "functional importance" score to variants with a default cutoff threshold of 0.05, with variants with a SIFT score higher than this threshold regarded as "benign".

Tagging of the region with an r threshold of 0.8 for variants with a MAF > 5%, 36 variants are required, but tagging at more aggressive r thresholds of 0.9 and 1.0 increased the number of tags to 39 and 116, respectively.

As an example, we explore the effect of varying the quality thresholds for variant calling using the NovoAlign/Samtools pipeline (Fig. 2).

To test the limits of SNP detection, discovery by setting a minimum variant threshold of 10% was also performed.

This is because these two features were computed after Samtools internal base quality filter threshold of 13, and the variant alleles had small base qualities so they did not pass this filter.