In mmaitenat/ideafix: ideafix, DEAmination FIXing

knitr::opts_chunk$set(echo = TRUE)

IDEAFIX

Overview

ideafix is a decision tree-based variant refinement tool that filters formaldehyde-induced cytosine deaminations from variant lists obtained from DNA sequencing data from FFPE specimens.

Installation

Installation may take a while...

if (!require("devtools")) install.packages("devtools")
devtools::install_github("mmaitenat/ideafix")

Requirements

ideafix needs the following programs to run:

bcftools
samtools (>1.8)

It also depends on the following packages:

h2o 3.22.1.1

ideafix also needs the following files:

VCF file obtained from an FFPE specimen. Variant calling needs to be run with Mutect2, with strand bias annotation enabled. It can be either a tumor-only or a normal-tumor paired variant calling.
Fasta file of the genome data was aligned to. If data is unaligned, the genome to align the data to.

If variant calling is to be run from bam files (feature not available yet), you will also need:

GATK4

Example

library(ideafix)
# Extract descriptors from vcf filename
vcf_filename <- "/home/maitena/Research/FFPE/code/ideafix/ideafix/inst/extdata/SRR1523260_filtermarks_annotated.vcf"
ref_genome <- "/home/maitena/Research/Data/RefGenomes/hg19/ucsc.hg19.fasta"
descriptors <- get_descriptors(vcf_filename = vcf_filename, fasta_filename = ref_genome)
# Filter C:G > T:A variants
predictions <- filter_variants(variant_descriptors = descriptors)