correctHetInv: Correct heterozygous inversion in StrandPhaseR VCF file.

In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

Correct heterozygous inversion in StrandPhaseR VCF file.

Description

This function takes as an input region deemed to be a heterozygous inversion along with phased SNVs within a region and uses this information to add/correct into the StrandPhaseR formatted VCF file.

Usage

correctHetInv(correct.gr = NULL, vcf.file = NULL, het.haps = NULL, ID = "")

Arguments

correct.gr	A GRanges object of homozygous inversion site to be corrected.
vcf.file	A StrandPhaseR formatted VCF file to be corrected for inversion phasing.
het.haps	A data.frame with phased alleles per inverted and reference haplotype.
ID	A unique id to be appended at the end of each corrected VCF file.

Value

NULL

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on April 7, 2024, 7:13 p.m.