readGATK {vanquish}

Read in input vcf data in GATK format for Contamination detection

Description

Read in input vcf data in GATK format for Contamination detection

Usage

readGATK(dr, dbOnly, depCut, thred, content, extnum, keepall)

Arguments

dr

A valid input object

dbOnly

Use dbSNP as filter, default is FALSE, passed from read_vcf

depCut

Use a threshold for min depth , default is False

thred

Threshold for min depth, default is 20

content

Column names in VCF files

extnum

The column number or numbers to be extracted from vcf, default is 10; 0 for not extracting any columns

keepall

Keep unextracted column in output, default is TRUE, passed from read_vcf

Value

Dataframe from VCF file