read.all.calls: read.all.calls

In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description

Read all calls made with a certain caller

Usage

read.all.calls(sample.ids, caller = c("vardict", "mutect", "pgm"),
  project.directory, patient.ids = NULL, apply.filters = TRUE,
  variant.file.pattern = NULL)

Arguments

sample.ids	Vector giving sample IDs to process
caller	String indicating which caller was used
project.directory	Path to project directory
patient.ids	Optional vector giving patient ID (or other group) corresponding to each sample
apply.filters	Logical indicating whether filters specified in VariTAS options should be applied. Defaults to TRUE. !
variant.file.pattern	Pattern indicating where the variant file can be found. Sample ID should be indicated by SAMPLE_ID

Value

combined.variant.calls Data frame with variant calls from all patients

varitas documentation built on Nov. 14, 2020, 1:07 a.m.