vcfcomp: Compare two VCF/BCF files reporting various statistics

In vcfppR: Rapid Manipulation of the Variant Call Format (VCF)

Compare two VCF/BCF files reporting various statistics

Description

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": pearson correlation coefficient ** 2. "f1": F1-score, good balance between sensitivity and precision. "nrc": Non-Reference Concordance rate "pse": 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

Details

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

Value

a list of various statistics

Author(s)

Zilong Li [e-mail]

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)

vcfppR documentation built on Sept. 30, 2024, 1:06 a.m.