hetTgen: Generate allele depth or genotype table

In rCNV: Detect Copy Number Variants from SNPs Data

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
)

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

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.

Value

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

Author(s)

Piyal Karunarathne, Klaus Schliep

Examples

## Not run: vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf)
## End(Not run)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.