4. Investigating Filter ChainsΒΆ

The VCF data imported into the project using the ACMG Trio Template resulted in 50,691 variants, which are applied to the filter chain for variant quality control (Variant QC) and then the Inheritance Model. The inheritance model includes: Dominant de Novo, Dominant Inherited, Recessive Homozygous, Ressessive Compound Heterozygous, X-Linked, and Pathogenic in Incidental Finding (IF) Genes.For this project we will focus on variants present in the proband but if we wanted to change the sample you can click on the dropdown icon, highlighted in Figure 4-1, to view the other samples.

Project interface

Figure 4-1: Trio workflow interface.

Lets take a look at the first filter container titled Variant QC. The Variant QC filter logic can be expanded by clicking the square box icon in the upper right corner of the filter logic. All 50,691 variants are applied to this filter card which includes filtering on Read Depth (DP) >10 and Genotype Qualities (GQ) >20. These fields are derived from the sample field from the variant table. To add a field, right click on the column header and select Add to Filter Chain. You can also delete filter cards by right clicking on the filter card in the filter chain and selecting Delete. Using this filter logic resulted in a total of 48,521 variants, which are then passed into the Inheritance Model filter container.

Variant quality control filter.

Figure 4-2: Variant quality control filter.

Next, we will deep dive into the first inheritance filter container, variants of Dominant de Novo inheritance. For easier viewing, minimize the Variant QC filter container, using the minimize icon, highlighted in Figure 4-2.