filter_biallelic

This function simply removes any SNPs from the vcf file which contains more than
two alleles. Many downstream applications require
SNPs to be biallelic, so this filter is generally a good idea during processing.

Is designed to interactively and reproducibly visualize and filter SNP
(single-nucleotide polymorphism) datasets. This R-based implementation of SNP
and genotype filters facilitates
an interactive and iterative SNP filtering pipeline, which can be documented
reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing
various quality and missing data metrics for a SNP dataset, and then filtering
the dataset based on user specified cutoffs.
All functions take 'vcfR' objects as input, which can easily be
generated by reading standard vcf (variant call format) files into R using
the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>).
Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be
written to a local directory in standard vcf format using the 'vcfR' package,
for downstream population genetic and phylogenetic analyses.

Devon DeRaad

SNPfiltR

Interactively Filter SNP Datasets

filter_biallelic function

<dl><dt>vcfR</dt>
<dd>a vcfR object</dd></dl>

Arguments

Remove SNPs with more than two alleles — filter_biallelic

<dl>

<dt>vcfR</dt>
<dd>a vcfR object</dd>

</dl>

filter_biallelic: Remove SNPs with more than two alleles

Description

Usage

Value

Arguments

Examples