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

VariantFiltering-packageR Documentation

Filtering of coding and non-coding genetic variants


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.


  • 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.


Dei M. Elurbe and Robert Castelo.

Maintainer: Robert Castelo <>


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

rcastelo/VariantFiltering documentation built on Nov. 29, 2023, 10:30 p.m.