Compare two VCF/BCF files reporting various statistics

Usage

vcfcomp(
  test,
  truth,
  formats = c("DS", "GT"),
  stats = "r2",
  by.sample = FALSE,
  by.variant = FALSE,
  flip = FALSE,
  names = NULL,
  bins = NULL,
  af = NULL,
  out = NULL,
  choose_random_start = FALSE,
  return_pse_sites = FALSE,
  ...
)

Arguments

test: path to the comparision file (test), which can be a VCF/BCF file, vcftable object or saved RDS file.
truth: path to the baseline file (truth),which can be a VCF/BCF file, vcftable object or saved RDS file.
formats: character vector. the FORMAT tags to extract for the test and truth respectively. default c("DS", "GT") extracts 'DS' of the target and 'GT' of the truth.
stats: the statistics to be calculated. supports the following. "r2": the Pearson correlation coefficient square. "f1": the F1-score, good balance between sensitivity and precision. "nrc": the Non-Reference Concordance rate "pse": the Phasing Switch Error rate
by.sample: logical. calculate sample-wise concordance, which can be stratified by MAF bin.
by.variant: logical. calculate variant-wise concordance, which can be stratified by MAF bin. If by.sample is TRUE, then do sample-wise calculation only regardless the value of by.variant. If both by.sample and by.variant are FALSE, then do calculations for all samples and variants together in a bin.
flip: logical. flip the ref and alt variants
names: character vector. reset samples' names in the test VCF.
bins: numeric vector. break statistics into allele frequency bins.
af: file path to allele frequency text file or saved RDS file.
out: output prefix for saving objects into RDS file
choose_random_start: choose random start for stats="pse"
return_pse_sites: boolean. return phasing switch error sites
...: options passed to vcftable

Value

a list of various statistics

Details

vcfcomp implements various statisitcs to compare two VCF/BCF files, e.g. report genotype concocrdance, correlation stratified by allele frequency.

Author

Zilong Li zilong.dk@gmail.com

Examples

library('vcfppR')
test <- system.file("extdata", "imputed.gt.vcf.gz", package="vcfppR")
truth <- system.file("extdata", "imputed.gt.vcf.gz", package="vcfppR")
samples <- "HG00133,HG00143,HG00262"
res <- vcfcomp(test, truth, stats="f1", samples=samples, setid=TRUE)
str(res)