correctHetInv: Correct heterozygous inversion in StrandPhaseR VCF file.
In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

View source: R/correctInversionPhasing.R

correctHetInv

R Documentation

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.