filter_vcf: Filter a vcfR object

In Neato-Nick/mllR:

Filter a vcfR object

Description

Filter a vcfR object

Usage

filter_vcf(
  x,
  min_depth = 4,
  max_depth = 800,
  min_mq = 20,
  samples_miss1 = 0.9999,
  samples_miss2 = 0.7,
  vars_miss = 0.2,
  top_dp_quantile_filter = TRUE,
  remove_nonpolymorphs = TRUE,
  cleanup = TRUE
)

Arguments

x	a vcfR object
min_depth	Minimum depth a genotype call must be to not be censored.
max_depth	Maximum depth a genotype call can be or else it wil be censored.
min_mq	Minimum mapping quality a genotype call can be or else it will be censored.
samples_miss1	Maximum percent missing data a sample can have before it gets omitted. Occurs before variant omission.
samples_miss2	Maximum percent missing data a sample can have before it gets omitted. Occurs after variant omission.
vars_miss	Maximum percent missing data a variant can have before it gets omitted. Occurs after first wave of sample omission.
remove_nonpolymorphs	After removing samples, some variants will no longer be polymorphic. These should be removed to not inflate the true number of variants.
cleanup	If TRUE (default), remove temporary VCFs from memory and perform garbage cleanup. Almost necessary for large VCFs (>100 MB)
top_95_quantile_filter	Censor the 5th and 95th percentiles of genotype call depth or not.

Value

A filtered vcfR object.

Examples

filtered_vcf <- filter_vcf(unfiltered_vcf)
filtered_vcf <- filter_vcf(unfiltered_vcf, samples_miss1 = 0.8, samples_miss2 = 0.4, vars_miss = 0.001)

Neato-Nick/mllR documentation built on Aug. 30, 2024, 7:22 a.m.