readGATK

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

dbOnly

Use a threshold for min depth , default is False

depCut

Threshold for min depth, default is 20

thred

content

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

extnum

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

keepall

Read in input vcf data in GATK format for Contamination detection

Imports Variant Calling Format file into R. It can detect
whether a sample contains contaminant from the same species.
In the first stage of the approach, a change-point detection
method is used to identify copy number variations for filtering.
Next, features are extracted from the data for a support vector
machine model. For log-likelihood calculation, the deviation
parameter is estimated by maximum likelihood method. Using
a radial basis function kernel support vector machine, the
contamination of a sample can be detected.

readGATK: Read in input vcf data in GATK format for Contamination detection

Description

Usage

Arguments

Value