download_clinvar: Import ClinVar VCF

In jamesdiao/clinvaR: collection, analysis, and visualization tools for ClinVar data

Description

This function allows you to read a ClinVar VCF into a table and extract important information from the INFO section.

Usage

download_clinvar()
download_clinvar(file)

Arguments

file	character; specifies the path to the VCF.

Details

getclinvar() collects the latest VCF from 'ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz' Specifying a file path will collect the VCF from that path instead.

Examples

clinvar <- sprintf("ClinVar_Reports/VCF/clinvar_%s.vcf.gz", clinvar_date) %>% 
              download_clinvar(file)
clinvar <- clinvar[!duplicated(clinvar$VAR_ID),] # remove duplicates

jamesdiao/clinvaR documentation built on May 18, 2019, 11:19 a.m.