Description Usage Arguments Details Examples
This function allows you to read a ClinVar VCF into a table and extract important information from the INFO section.
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file |
character; specifies the path to the VCF. |
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.
1 2 3 | clinvar <- sprintf("ClinVar_Reports/VCF/clinvar_%s.vcf.gz", clinvar_date) %>%
download_clinvar(file)
clinvar <- clinvar[!duplicated(clinvar$VAR_ID),] # remove duplicates
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