Check for CHIP variants in normal and tumour at high VAF

Source: R/check_CHIP_variants.R

Check for CHIP variants in normal and tumour at high VAF

check_CHIP_variants(
  normal_bam = NULL,
  tumour_bam = NULL,
  reference = "hg38",
  min_vaf = 0.05,
  only_snvs = TRUE,
  add_chr = TRUE
)

Arguments

normal_bam

path of bam file for healthy sample

tumour_bam

path of bam file for tumour sample

reference

reference genome, one of hg38 or hg19

min_vaf

minimum required VAF to flag the mutation

only_snvs

use only SVNs and filter indels

add_chr

if chromosomes on BAM files have chr set it to TRUE

The function takes a tumour and a normal bam files and scans for known CHIP mutations listed in Bick et al.. The function gives back a data frame with mutation having VAF higher than min_vaf. A bit of caution has to be taken when interpreting indels results, as from the pileup we cannot assign a lenght to the indel and the frameshit nature of the alteration. We suggest doing a proper small variant calling to confirm the results.

Value

Two dataframes for each of tumour and nomal with coloumns: chr, pos, alt, ref, VAF, DP and NV (chromosome, position, alternative allele, reference allele, variant allelic frequency, depth , number of variant reads)