get_var_annotation: Extract variant annotation

In santiago1234/phdpopgene: What the Package Does (One Line, Title Case)

Description

This function extracts the variant annotation FUNSEQ and Consequence from the annotation vcf data

Usage

get_var_annotation(vcf_genotypes, vcf_annotation, chrn)

Arguments

vcf_genotypes	CollapsedVCF, genotypes vcf
vcf_annotation	CollapsedVCF -> VariantAnnotation::readVcf. The annotaion for the variants in vcf_genotypes
chrn	int or chr, chromosome name

Value

A data frame

varid

Variant ID

range_id

Id for variant in range chrn:start_RF/ALT

Consequence

Calculated variant consequence

FUNSEQ

FUNSEQ score

Examples

get_var_annotation(test_vcf, test_anno_vcf, 22)

santiago1234/phdpopgene documentation built on Dec. 31, 2020, 5:06 a.m.