read_vcf {sssc}

VCF Data Input

Description

Reads a file in vcf or vcf.gz file and creates a list containing Content, Meta, VCF and file_sample_name

Usage

read_vcf(fn, vcffor, dbOnly = FALSE, depCut = FALSE, thred = 20,
  metaline = 200, extnum = 10, keepall = T)

Arguments

fn

Input vcf file name

vcffor

Input vcf data format: 1) GATK; 2) VarPROWL; 3) VarDict; 4) strelka2

dbOnly

Use dbSNP as filter, default is FALSE

depCut

Use a threshold for min depth , default is False

thred

Threshold for min depth, default is 20

metaline

Number of head lines to read in (better to be large enough), the lines will be checked if they contain meta information, default is 200

extnum

The column number to be extracted from vcf, default is 10; 0 for not extracting any column; extnum should be between 10 and total column number

keepall

Keep unextracted column in output, default is TRUE

Value

A list containing (1) Content: a vector showing what is contained; (2) Meta: a data frame containing meta-information of the file; (3) VCF: a data frame, the main part of VCF file; (4) file_sample_name: the file name and sample name, in case when multiple samples exist in one file, file and sample names might be different

Examples

file.name <- system.file("extdata", "example.vcf.gz", package = "sssc")
example <- read_vcf(fn=file.name, vcffor="VarPROWL")