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. DefaultAD, See details.- verbose
logical. whether to show the progress of the analysis
- parallel
logical. whether to parallelize the process
Value
Returns a data frame of allele depth, genotype of SNPs for all the individuals extracted from a VCF file
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
vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf)
#> generating table
#>
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