filter_exac_variants_by_cadd: filter ExAC variants by CADD score

Description Usage Arguments Value

View source: R/filter_by_CADD.R

Description

filter ExAC variants by CADD score

Usage

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filter_exac_variants_by_cadd(vars,
  path = "/lustre/scratch115/projects/ddd/users/hcm/DDD/CADD_resources/ExAC_r0.3.tsv.gz",
  threshold = 21, exclude = FALSE,
  tempdir = "/lustre/scratch115/projects/ddd/users/hcm/DDD/tempdir_for_gene_vcfs_for_annotation/",
  notLoFs = TRUE)

Arguments

vars

data frame or list of data frames with ExAC variants, output from get_exac_variants_for_gene

path

path to vcf.gz file of CADD scores, default = /lustre/scratch115/projects/ddd/users/hcm/DDD/CADD_resources/ExAC_r0.3.tsv.gz

threshold

CADD score cutoff for variants, default = 21

exclude

boolean for whether to exclude variants without a CADD score, default=FALSE

tempdir

path to temporary diectory for writing VCF files; default = /lustre/scratch115/projects/ddd/users/hcm/DDD/tempdir_for_gene_vcfs_for_annotation/

notLoFs

boolean for whether to keep all LoFs regardless of CADD score, default = TRUE

Value

data frame or list of data frame with ExAC variants, filtered by CADD


jeremymcrae/recessiveStats documentation built on May 17, 2017, 6:09 p.m.