vcfsummary: summarize the various variant types at both variant level and...

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

summarize the various variant types at both variant level and sample level.

Description

summarize the various variant types at both variant level and sample level.

Usage

vcfsummary(
  vcffile,
  region = "",
  samples = "-",
  pass = FALSE,
  qual = 0,
  svtype = FALSE
)

Arguments

vcffile	path to the VCF/BCF file
region	region to subset like bcftools
samples	samples to subset like bcftools
pass	restrict to variants with FILTER==PASS
qual	restrict to variants with QUAL > qual.
svtype	summarize the variants with SVTYPE

Details

bcftools view -s "id01,id02" input.bcf.gz chr1:100000-20000

Value

vcfsummary a list containing the following components:

summary

: named integer vector;
summarize the counts of each variant type

samples

: character vector;
the samples ids in the VCF file after subsetting

vartype

: integer vector;
the counts of the variant type at sample level in the same order as samples

Author(s)

Zilong Li [e-mail]

Examples

library('vcfppR')
svfile <- system.file("extdata", "sv.vcf.gz", package="vcfppR")
res <- vcfsummary(svfile, region = "chr21:1-10000000", svtype = TRUE)
str(res)

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