CNproScanCNV: CNproScan - CNV detection for bacteria genomes This function...

In robinjugas/CNproScan: CNproScan detects and annotates CNVs in bacterial genomes.

CNproScan - CNV detection for bacteria genomes This function detects and annotate CNVs in bacterial genomes. It uses GESD outliers detection and detection of discordant read-pairs for annotation.

Description

CNproScan - CNV detection for bacteria genomes This function detects and annotate CNVs in bacterial genomes. It uses GESD outliers detection and detection of discordant read-pairs for annotation.

Usage

CNproScanCNV(
  coverageFile,
  bamFile,
  fastaFile,
  GCnorm = TRUE,
  MAPnorm = FALSE,
  ORICnorm = FALSE,
  bedgraphFile = NULL,
  oriCposition = 0,
  cores = 2
)

Arguments

coverageFile	Path to the coverage file given from samtools depth. Zeroe values must be included, use -a switch "samtools depth -a".
bamFile	Path to the BAM file, sorted and indexed.
fastaFile	Path to the reference FASTA file used to align sequencing reads. The headers should be the same through all input files (FASTA, BAM and COVERAGE files).
GCnorm	Should the GC normalization be performed. Logical value. Default is TRUE.
MAPnorm	Should the genome mappability normalization be performed. Default is FALSE. If TRUE, the argument bedgraphFile must be specified.
bedgraphFile	Path to the bedgraph file outputed from genmap tool.
cores	number of cores to be used by parallel package. Default is two. Decreases computation time with limited impact on RAM usage.

Value

A dataframe of detected CNVs and VCF file name as sample_cnproscan.vcf in the working directory.

robinjugas/CNproScan documentation built on April 11, 2024, 7:15 p.m.