read.all.calls {varitas}

read.all.calls

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