rCNV (version 1.3.0)

hetTgen: Generate allele depth or genotype table

Description

hetTgen extracts the read depth and coverage values for each snp for all the individuals from a vcf file generated from readVCF (or GatK VariantsToTable: see details)

Usage

hetTgen(
  vcf,
  info.type = c("AD", "AD-tot", "GT", "GT-012", "GT-AB", "DP"),
  verbose = TRUE,
  parallel = FALSE
)

Value

Returns a data frame of allele depth, genotype of SNPs for all the individuals extracted from a VCF file

Arguments

vcf

an imported vcf file in a list using readVCF

info.type

character. AD: allele depth value, AD-tot:total allele depth, DP=unfiltered depth (sum), GT: genotype, GT-012:genotype in 012 format, GT-AB:genotype in AB format. Default AD, See details.

verbose

logical. whether to show the progress of the analysis

parallel

logical. whether to parallelize the process

Author

Piyal Karunarathne, Klaus Schliep

Details

If you generate the depth values for allele by sample using GatK VariantsToTable option, use only -F CHROM -F POS -GF AD flags to generate the table. Or keep only the CHROM, POS, ID, ALT, and individual AD columns. For info.type GT option is provided to extract the genotypes of individuals by snp.

Examples

if (FALSE) vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf)