Import intervals from a VCF file

Source: R/intervals-import.R

Reads a VCF/VCF.gz file and returns a misha 1D intervals data frame with one row per record. VCF is 1-based; start is set to POS - 1 and end is set to POS - 1 + nchar(REF), yielding a 0-based half-open span covering the reference allele.

gintervals.import_vcf(file = NULL, info = TRUE)

Arguments

file

path to a VCF/VCF.gz file.

info

if TRUE, include the raw INFO column as info. The string is not parsed.

Value

A 1D intervals data frame with columns chrom, start, end, and id, ref, alt, qual, filter, optionally info.

Details

Chromosome names are normalized through the active database's CHROM_ALIAS mechanism.

Multi-allelic records are kept as a single row; the ALT column contains the original comma-separated string.