In Hatoonli/vcfqc: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

vcfqc

vcfqc is a tool that can visualize the distribution of quality annotation values in a table summary of VCF files. This visualization can help in setting threshhold values for hard-filtering.

Installation

You can install the latest version of vcfqc by copying the following commands into R console:

library(devtools)
devtools::install_github("Hatoonli/vcfqc", build_vignettes = TRUE)

Example

This is an example of quality by depth (QD) annotation distribution

library(vcfqc)
QD(system.file("extdata", "HG001_GRCh38.table", package = "vcfqc"))

Hatoonli/vcfqc documentation built on May 16, 2022, 12:19 p.m.