filter_SNPindex: Filter SNP-index Variants

In EG-lisy/BSAvis: Bulk Segregant Analysis - Visualisation Package

Description

This function filters out variants in the data frame returned by the calc_SNPindex() function which do not fall between minimum DP, maximum DP, minimum SNP-index, maximum SNP-index, and minimum GQ for both bulks (wild-type and mutant).

Usage

filter_SNPindex(
  vcf.df.SNPindex,
  min.SNPindex = 0.3,
  max.SNPindex = 0.9,
  min.DP = 50,
  max.DP = 200,
  min.GQ = 99
)

Arguments

vcf.df.SNPindex	vcf dataframe
min.SNPindex	min value allowed for the SNP index (default=0.3)
max.SNPindex	max value allowed for the SNP index (default=0.9)
min.DP	min value allowed for the read depth (default=50)
max.DP	max value allowed for the read depth (default=200)
min.GQ	min value allowed for the genotype quality (default=99)

Details

Variants from the data frame returned by the calc_SNPindex() function are filtered out based on the following criteria: minimum DP, maximum DP, minimum SNP-index, maximum SNP-index, and minimum GQ.

Variants must pass these filters in both bulks to be retained.

Value

data frame containing variant and SNP-index information on variants that passed the filtering process.

Examples

## Default parameters
vcf_df_SNPindex_filt <- filter_SNPindex(vcf.df.SNPindex=vcf_df_SNPindex)
## Custom parameters
vcf_df_SNPindex_filt <- filter_SNPindex(vcf.df.SNPindex=vcf_df_SNPindex, 
                                        min.SNPindex=0.25, 
                                        max.SNPindex=0.8, 
                                        min.DP=60, 
                                        max.DP=250, 
                                        min.GQ=98)

EG-lisy/BSAvis documentation built on Dec. 17, 2021, 5:38 p.m.