gtMarkers: Extract read counts from genetic markers for ASCAT analysis

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Extract read counts from genetic markers for ASCAT analysis

Description

The function will generate tsv files '<tumor/normal>_nucleotide_counts.tsv' that can be used for downstream analysis. Note that the function will process ~900K loci from Affymetrix Genome-Wide Human SNP 6.0 Array. The process can be sped up by increasing 'nthreads' which will launch each chromosome on a separate thread. Currently hg19 and hg38 are supported. Files need to be further processed with prepAscat for tumor-normal pair, or prepAscat_t for tumor only samples.

Usage

gtMarkers(
  t_bam = NULL,
  n_bam = NULL,
  build = "hg19",
  prefix = NULL,
  add = TRUE,
  mapq = 10,
  sam_flag = 1024,
  loci = NULL,
  fa = NULL,
  op = NULL,
  zerobased = FALSE,
  nthreads = 4,
  verbose = TRUE
)

Arguments

t_bam	Tumor BAM file. Required
n_bam	Normal BAM file. Recommended
build	Default hg19. Mutually exclusive with 'loci'. Currently supported 'hg19' and 'hg38' and includes ca. 900K SNPs from Affymetrix Genome-Wide Human SNP 6.0 Array. SNP file has no 'chr' prefix.
prefix	Prefix to add or remove from contig names in loci file. For example, in case BAM files have ‘chr' prefix, set prefix = ’chr'
add	If prefix is used, default is to add prefix to contig names in loci file. If false prefix will be removed from contig names.
mapq	Minimum mapping quality. Default 10
sam_flag	SAM FLAG to filter reads. Default 1024
loci	A tab separated file with chr and position. If not available use 'build' argument.
fa	Indexed fasta file. If provided, extracts and adds reference base to the output tsv.
op	Output file basename. Default parses from BAM file
zerobased	are coordinates zero-based. Default FALSE. Use only if 'loci' is used.
nthreads	Number of threads to use. Default 4. Each chromosome will be launched on a separate thread. Works only on Unix and macOS.
verbose	Default TRUE

See Also

prepAscat prepAscat_t segmentLogR

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.