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Read a VCF file into a data.table, caller-agnostically

Source: R/read_vcf.R
read_vcf.Rd

Reads the body of a VCF file (lines after #CHROM) into a data.table. The resulting table has whatever columns the VCF has (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, and optionally FORMAT plus one or more sample columns), with #CHROM renamed to CHROM.

Usage

read_vcf(file, filter = TRUE, name_of_vcf = NULL)

Arguments

file

Path or URL to the VCF file.

filter

Controls which rows are kept based on the FILTER column:

  • TRUE (default): keep rows where FILTER %in% c("PASS", ".", "") — the union of passing values across common callers.

  • FALSE or NULL: keep all rows.

  • A character vector: keep rows where FILTER %in% filter. Rows with no FILTER column are always kept; a warning is emitted when filter is non-trivial in that case.

name_of_vcf

Optional name for the VCF, used only for warning / error messages. Defaults to the filename with extension stripped.

Value

A data.table with one row per variant. The name of the first column is 'CHROM', not '#CHROM'. Other column names

Details

Caller-agnostic. read_vcf() does not know or care which variant caller produced the VCF. It does not parse FORMAT/sample columns and does not extract VAF or read depth. The only caller-dependent semantics is the default value of the filter argument (see below).

Uses data.table::fread() with check.names=FALSE, na.strings = ""``, fill = TRUE`, to parse the VCF body. Handles uncompressed and gzipped files; does not handle bgzipped/tabix.