callvar: callvar

In macs3-project/MACSr: MACS: Model-based Analysis for ChIP-Seq

callvar

Description

Call variants in given peak regions from the alignment BAM files.

Usage

callvar(
  peakbed,
  tfile,
  cfile,
  outputfile = character(),
  GQCutoffHetero = 0,
  GQCutoffHomo = 0,
  Q = 20,
  maxDuplicate = 1L,
  fermi = "auto",
  fermiMinOverlap = 30L,
  top2allelesMinRatio = 0.8,
  altalleleMinCount = 2L,
  maxAR = 0.95,
  np = 1L,
  verbose = 2L,
  log = TRUE
)

Arguments

peakbed	Peak regions in BED format, sorted by coordinates. REQUIRED.
tfile	ChIP-seq/ATAC-seq treatment file in BAM format, sorted by coordinates. Make sure the .bai file is avaiable in the same directory. REQUIRED.
cfile	Optional control file in BAM format, sorted by coordinates. Make sure the .bai file is avaiable in the same directory.
outputfile	Output VCF file name.
GQCutoffHetero	Genotype Quality score (-10log10((L00+L11)/(L01+L00+L11))) cutoff for Heterozygous allele type. Default:0, or there is no cutoff on GQ.
GQCutoffHomo	Genotype Quality score (-10log10((L00+L01)/(L01+L00+L11))) cutoff for Homozygous allele (not the same as reference) type. Default:0, or ther is no cutoff on GQ.
Q	Only consider bases with quality score greater than this value. Default: 20, which means Q20 or 0.01 error rate.
maxDuplicate	Maximum duplicated reads allowed per mapping position, mapping strand and the same CIGAR code. Default: 1. When sequencing depth is high, to set a higher value might help evaluate the correct allele ratio.
fermi	Option to control when to apply local assembly through fermi-lite. By default (set as 'auto'), while callvar detects any INDEL variant in a peak region, it will utilize fermi-lite to recover the actual DNA sequences to refine the read alignments. If set as 'on', fermi-lite will be always invoked. It can increase specificity however sensivity and speed will be significantly lower. If set as 'off', Fermi won't be invoked at all. If so, speed and sensitivity can be higher but specificity will be significantly lower. Default: auto
fermiMinOverlap	The minimal overlap for fermi to initially assemble two reads. Must be between 1 and read length. A longer fermiMinOverlap is needed while read length is small (e.g. 30 for 36bp read, but 33 for 100bp read may work). Default:30
top2allelesMinRatio	The reads for the top 2 most frequent alleles (e.g. a ref allele and an alternative allele) at a loci shouldn't be too few comparing to total reads mapped. The minimum ratio is set by this optoin. Must be a float between 0.5 and 1. Default:0.8 which means at least 80%% of reads contain the top 2 alleles.
altalleleMinCount	The count of the alternative (non-reference) allele at a loci shouldn't be too few. By default, we require at least two reads support the alternative allele. Default:2
maxAR	The maximum Allele-Ratio allowed while calculating likelihood for allele-specific binding. If we allow higher maxAR, we may mistakenly assign some homozygous loci as heterozygous. Default:0.95
np	CPU used for mutliple processing. Please note that, assigning more CPUs does not guarantee the process being faster. Creating too many parrallel processes need memory operations and may negate benefit from multi processing. Default: 1
verbose	Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2
log	Whether to capture logs.

Value

macsList object.

Examples

## Not run: 
callvar(
"PEsample_peaks_sorted.bed",
"PEsample_peaks_sorted.bam",
"PEcontrol_peaks_sorted.bam",
"/tmp/test.vcf")

## End(Not run)

macs3-project/MACSr documentation built on Sept. 24, 2024, 11:09 p.m.