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.
Defined environment variable:
R Dependence:
Extra Dependence:
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'))
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.
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.
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