check_CHIP_variants: Check for CHIP variants in normal and tumour at high VAF

In caravagn/TINC: TINC - Tumour-in-Normal contamination assessment

Check for CHIP variants in normal and tumour at high VAF

Description

Check for CHIP variants in normal and tumour at high VAF

Usage

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)

caravagn/TINC documentation built on April 28, 2024, 7:42 a.m.