flag_variants: Flag and annotate variants using external databases and panel...

In annaquaglieri16/samplepower: Compute sensitivity and false positive rates for a variant call set with repsect to a truth dataset.

Description

Flag and annotate variants using external databases and panel of normals information

Usage

flag_variants(variants, normal_variants, flag_patterns, exon_ranges,
  homop_ranges, RNAedit_ranges, repeats_ranges, flag_qualities = TRUE)

Arguments

variants	dataframe containing all the variants in the cohort. This is created within the 'variants_power()' function
normal_variants	link to panel of normal file parsed with 'samplepower::parse_pon'
flag_patterns	dataframe containing the flags to assign to variants. THIS NEEDS TO BE SET AS INTERNAL TO THE PACKAGE
exon_ranges	GRanges object with exon boundaries relative to the reference genome used
homop_ranges	GRanges object with homopolymers regions of more than 5bp relative to the reference genome used
RNAedit_ranges	GRanges object with RNA editing sites relative to the reference genome used
repeats_ranges	GRanges object with repetitive regions of the reference genome used
flag_qualities	logical. TRUE by default, variants are flagged based on quality measures. If FALSE this step is skipped.

annaquaglieri16/samplepower documentation built on Nov. 7, 2019, 11:43 p.m.