VariantFiltering-package:
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
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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.
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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.
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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.
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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.
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deNovo identify variants in the affected
individual that have not been inherited.
unrelatedIndividuals annotate variants without filtering by any inheritance pattern.
References
Elurbe D.M., Mila, M., Castelo, R. VariantFiltering: filtering of coding and non-coding genetic variants, in preparation.