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README.md

QualityConfirm

Introduction

QualityConfirm is a quality control tool for gene panel sequencing data. It relies on RColorBrewer, ggplot2, and stringr R packages. It also uses samtools to extract the depth of each base from bam files.

Guide

Defined environment variable:

  • SAMTOOLS, Path of samtools executable file
  • REFFA, Path of reference genome

R Dependence:

  • ggplot2
  • stringr
  • RColorBrewer

Extra Dependence:

  • samtools
  • reference genome
install.packages(c('ggplot2', 'stringr', 'RColorBrewer'))
setwd(dirname(system.file("extdata", "tools/QualityConfirm", package = "ngstk")))
Sys.setenv(SAMTOOLS = "/path/samtools", REFFA='/path/hg19')
source('demo.R')

## Object Initialization
Obj <- new("ReadsCheck", list(panelBed = './example/APL_panel.bed',
           bamDir = './example', resultDir='./example/result'))

Object

QualityConfirm defined a S4 object ReadsCheck. This object has 15 slots which can be classified into 5 groups:

  • Environment

    • samtools: the path to samtools, default samtools.

    • refhg: the path to human genome, default hg19.fa.

  • Input Directories or Files

    • panelBed: the path to bed files, default scanning the .bed file in the current dir.

    • bamDir: the path to the directory of all bam files, default current dir.

    • bamList: bam files need to analysis, default to scanning all .bam files in the bamDir.

  • Program Parameters

    • maxDepth: the parameters used in samtools, default 40000.

    • bedGap: the parameters deciding to how to merge the original panel, default 2.

  • Output Directories

    • resultDir: the result directory, default ./result.

    • depthDir: the depth data files directory, would set to resultDir/depth.

    • figDir: the gene coverage diretory, would set to resultDir/fig.

    • sumDir: the summary diretory, would set to resultDir/summary.

    • mergeBedPath: the merged panel bed file, would set to resultDir/merge.panel.bed.

  • Other

    • currBamNum: the index of current process bam file, add 1 when finish SingleReadsSummary.

    • status: the process status of each bam, ReadsDepth add 1, PlotCountFig add 2, SingleReadsSummary add 4.

    • mergedBed: the data frame to store the merged panel.

Functions

QualityConfirm has 6 main functions:

  • PanelMerge: the function to merge panel.

  • PlotBedHist: the function to plot panel distribution.

  • ReadsDepth: the function to get depth data files. Give the test=TRUE for program testing without running samtools parameter.

  • PlotCountFig:the function to plot gene coverage figure.

  • SingleReadsSummary: the function to get the summary for each panel region in a sample.

  • AllReadsSummary: the function to get the summary of overall.

Every function will return the object with updating. And the inpute is only a defined object.

Maintainer