Remove SNPs with more than two alleles — filter

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.

filter_biallelic(vcfR)

Arguments

vcfR: a vcfR object

Value

a vcfR object with SNPs containing more than two alleles removed

Examples

filter_biallelic(vcfR = SNPfiltR::vcfR.example)
#> 0 SNPs, 0% of all input SNPs, contained more than 2 alleles, and were removed from the VCF

#> ***** Object of Class vcfR *****
#> 20 samples
#> 1 CHROMs
#> 500 variants
#> Object size: 0.7 Mb
#> 38.07 percent missing data
#> *****        *****         *****