filter_VCF_SNPs: Function to filter variants in VCF files based on column 2...

In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Description

This function read the whole vcf file, filter out variants and return the genotype likelihood in VCF file for case and control separately. it calls get_likelihood_vcf to convert the vcf format into phred score. The keeping criteria are: variants that PASS filters, do not have duplicates, have only one reference allele with missing rate <=missing_th missing rate.

Usage

filter_VCF_SNPs(vcf_file, caseID_file, nvars = 1000, nread = 300,
  nhead = 128, ncol_ID = 9, missing_th = 0.5)

Arguments

vcf_file	The saving address and filename of the vcf file in the format of 'address/filename'.
caseID_file	The file including case IDs in the format of 'address/filename'.
nvars	total number of variants in the vcf file. default=1000
nread	each time the read.table will read nread number of rows in file, default=300
nhead	The number of the lines in the vcf file which started with #, default=128.
ncol_ID	default =9, the number of columns before each individual's data
missing_th	the missing rate for filter out a variant, default is set=0.5

Value

The function returns a list including 6 matrices and 2 vectors:

6 matrices:case00, case01, case11, cont00, cont01 and cont11 which contain the genotype likelihoods from VCF, 2 vectors for variant chromosome and location.

Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.