clonalityParsers

R package for parsing SNV and CNV calls for clonality analysis

Description

Clonality analysis requires providing SNV and CNV calls to the clonality analysis algorithm. Since there is a number of CNV and SNV callers and at least the same number of clonality analysis alorithms, there might be tens of parsing combinations required. This package is a container for functions parsing SNVs and CNVs to a kind of universal format, and for functions parsing the universally formated data to the format required by clonality algorithms, to facilitate interchangeability of the algorithms.

Supported algorithms

SNV callers:

• Mutect2

CNV callers:

• FACETS

Clonality analysis algorithms:

• PyClone-VI
• CliP

If you would like to get clonalityParsers support your algorithm, let me know in the Issues.

Installation

remotes::install_github("https://github.com/pawelqs/clonalityParsers.git")

Usage

R

library(clonalityParsers)

FACETS_files <- c(
  S1_P1 = system.file("testdata", "S1_P1.csv", package = "clonalityParsers"),
  S1_L1 = system.file("testdata", "S1_L1.csv", package = "clonalityParsers")
)
Mutect_file <- system.file("testdata", "S1_Mutect.vcf", package = "clonalityParsers")
S1_sample_ids <- c("S1_P1", "S1_L1")
S1_genome_build <- "hg38"
S1_sex <- "male"

td <- read_files(
  Mutect_file, FACETS_files,
  sample_ids = S1_sample_ids, sex = S1_sex, genome_build = S1_genome_build
)

td %>%
  filter_SNVs(filter_min_DP = 10) %>%
  prepare_pycloneVI_input(filename = "S1.pyclone-input.tsv")

Shell

An example script for shell usage is in inst/example, along with the conda environments.