Skip to main content
Figure 3 | BMC Bioinformatics

Figure 3

From: Effective filtering strategies to improve data quality from population-based whole exome sequencing studies

Figure 3

Improved Ti/ Tv ratios in WES data using variant filters. Plots illustrate Ti/Tv improvement at different thresholds of A) average GQ and B) call rate. In these plots, Ti/Tv ratios (blue) for novel (dotted line), known (dashed line) and true (solid line) variants are juxtaposed against the drop in sensitivity (red) as the variant filtering thresholds increase. Chosen thresholds are show by the red dashed lines. C) The Ti/Tv improvement after each of the variant filtering steps is summarized. In addition, the result from an alternative filtering order, where VQSR is applied prior to the combined variant filters, is also displayed (green circle). *Combined filters refers to HWE, average GQ and call rate filters applied together.

Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us