gintervals.import_vcf: Import intervals from a VCF file

In misha: Toolkit for Analysis of Genomic Data

Import intervals from a VCF file

Description

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.

Usage

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.

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.

Value

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

See Also

gintervals.import_bed, gintervals.import_gff.

misha documentation built on Aug. 24, 2026, 5:14 p.m.