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

VariantFiltering-package

R Documentation

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.