genotypeStrandScells: Genotype Strand-seq cell based on population genotypes.

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

Genotype Strand-seq cell based on population genotypes.

Description

This function will import variants (SNVs) covered in individual Strand-seq libraries in a form of BAM files aligned to a a reference genome such as GRCh38. Such SNVs are compared to a population genotypes such as 1000G sample panel.

Usage

genotypeStrandScells(
  inputfolder = NULL,
  strandS.vcf = NULL,
  popul.vcf.list = NULL,
  wc.regions = NULL,
  chromosomes = paste0("chr", c(1:22)),
  min.snv.cov = 5,
  max.snv.cov = 30,
  max.snv.per.chr = 30000,
  blacklist = NULL
)

Arguments

inputfolder	A data folder where individual Strand-seq BAM files are stored.
strandS.vcf	A VCF file that contains SNVs called from merged Strand-seq libraries using RTG tool.
popul.vcf.list	A names list of paths to VCF files (per chromosome) that contains SNVs from multiple individuals such as 1000G sample panel.
wc.regions	A Watson-crick regions per library and per chromosome as defined by breakpointR.
chromosomes	List of chromosomes to be used for genotyping.
min.snv.cov	A minumum number of Strand-seq reads required to cover a SNV position in 'strandS.vcf'.
max.snv.cov	A maximum number of Strand-seq reads allowed to cover a SNV position in 'strandS.vcf'.
max.snv.per.chr	A maximum number of SNVs to be loaded from population panel VCF ('popul.vcf) per chromosome.
blacklist	AGRanges-class object of genomic regions to filter out SNV positions.

Value

A data.frame object.

Author(s)

David Porubsky

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