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.

if (!require("devtools")) install.packages("devtools")
devtools::install_github("mmaitenat/ideafix", build_vignettes = TRUE)

ideafix needs the following programs to run:

• bcftools

• samtools

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.

library(ideafix)
# Extract C:G > T:A variants with a VAF < 30% and their descriptors from vcf filename
vcf_filename <- "mysample_chr15.vcf"
ref_genome <- "chr15.fasta"
descriptors <- get_descriptors(vcf_filename = vcf_filename, fasta_filename = ref_genome)
# Filter variants
predictions_XGBoost <- classify_variants(variant_descriptors = descriptors, algorithm = "XGBoost")