VariantFiltering-package: Filtering of coding and non-coding genetic variants

In rcastelo/VariantFiltering: Filtering of coding and non-coding genetic variants

Filtering of coding and non-coding genetic variants

Description

The VariantFiltering package filters coding and non-coding genetic variants using different criteria such as an inheritance model (autosomal recessive -both, homozygous and heterozygous-, autosomal dominant, X-linked and de novo), amino acid change consequence, minor allele frequencies, cryptic splice site potential, conservation, etc.

Functions

• autosomalRecessiveHomozygous identify homozygous variants in the affected individual(s) while the unaffected ones present these same variants but in heterozygous state. Autosomal recessive inheritance pattern.

• autosomalRecessiveHeterozygous identify variants grouped by genes with two (or more) heterogeneous alleles (at least one on each allele, i.e. coming from each parent). Autosomal recessive inheritance pattern.

• autosomalDominant identify variants present in all the affected individual(s) discarding the ones that also occur in at least one of the unaffected subjects. Autosomal dominant inheritance pattern.

• xLinked identify variants that appear only in the X chromosome of the unaffected females as heterozygous, don't appear in the unaffected males analyzed and finally are present (as homozygous) in the affected male(s). X-linked inheritance pattern.

• deNovo identify variants in the affected individual that have not been inherited.

• unrelatedIndividuals annotate variants without filtering by any inheritance pattern.

Author(s)

Dei M. Elurbe and Robert Castelo.

Maintainer: Robert Castelo <[e-mail]>

References

Elurbe D.M., Mila, M., Castelo, R. VariantFiltering: filtering of coding and non-coding genetic variants, in preparation.

rcastelo/VariantFiltering documentation built on Oct. 23, 2024, 5:23 p.m.