variantReport {systemPipeR} | R Documentation |
Functions for generating tabular variant reports including genomic context annotations and confidence statistics of variants. The annotations are obtained with utilities provided by the VariantAnnotation
package and the variant statistics are retrieved from the input VCF files.
## Variant report variantReport(args, txdb, fa, organism) ## Combine variant reports combineVarReports(args, filtercol, ncol = 15) ## Create summary statistics of variants varSummary(args)
args |
Object of class |
txdb |
Annotation data stored as |
fa |
|
organism |
Character vector specifying the organism name of the reference genome. |
filtercol |
Named character vector containing in the name field the column titles to filter on, and in the data field the corresponding values to include in the report. For instance, the setting |
ncol |
Integer specifying the number of columns in the tabular input files. Default is set to 15. |
Tabular output files.
Thomas Girke
filterVars
## Alignment with BWA (sequentially on single machine) param <- system.file("extdata", "bwa.param", package="systemPipeR") targets <- system.file("extdata", "targets.txt", package="systemPipeR") args <- systemArgs(sysma=param, mytargets=targets) sysargs(args)[1] ## Not run: system("bwa index -a bwtsw ./data/tair10.fasta") bampaths <- runCommandline(args=args) ## Alignment with BWA (parallelized on compute cluster) resources <- list(walltime=120, ntasks=1, ncpus=cores(args), memory=1024) reg <- clusterRun(args, conffile=".batchtools.conf.R", template="batchtools.slurm.tmpl", Njobs=18, runid="01", resourceList=resources) ## Variant calling with GATK ## The following creates in the inital step a new targets file ## (targets_bam.txt). The first column of this file gives the paths to ## the BAM files created in the alignment step. The new targets file and the ## parameter file gatk.param are used to create a new SYSargs ## instance for running GATK. Since GATK involves many processing steps, it is ## executed by a bash script gatk_run.sh where the user can specify the ## detailed run parameters. All three files are expected to be located in the ## current working directory. Samples files for gatk.param and ## gatk_run.sh are available in the subdirectory ./inst/extdata/ of the ## source file of the systemPipeR package. writeTargetsout(x=args, file="targets_bam.txt") system("java -jar CreateSequenceDictionary.jar R=./data/tair10.fasta O=./data/tair10.dict") # system("java -jar /opt/picard/1.81/CreateSequenceDictionary.jar R=./data/tair10.fasta O=./data/tair10.dict") args <- systemArgs(sysma="gatk.param", mytargets="targets_bam.txt") resources <- list(walltime=120, ntasks=1, ncpus=cores(args), memory=1024) reg <- clusterRun(args, conffile=".batchtools.conf.R", template="batchtools.slurm.tmpl", Njobs=18, runid="01", resourceList=resources) writeTargetsout(x=args, file="targets_gatk.txt") ## Variant calling with BCFtools ## The following runs the variant calling with BCFtools. This step requires in ## the current working directory the parameter file sambcf.param and the ## bash script sambcf_run.sh. args <- systemArgs(sysma="sambcf.param", mytargets="targets_bam.txt") resources <- list(walltime=120, ntasks=1, ncpus=cores(args), memory=1024) reg <- clusterRun(args, conffile=".batchtools.conf.R", template="batchtools.slurm.tmpl", Njobs=18, runid="01", resourceList=resources) writeTargetsout(x=args, file="targets_sambcf.txt") ## Filtering of VCF files generated by GATK args <- systemArgs(sysma="filter_gatk.param", mytargets="targets_gatk.txt") filter <- "totalDepth(vr) >= 2 & (altDepth(vr) / totalDepth(vr) >= 0.8) & rowSums(softFilterMatrix(vr))==4" # filter <- "totalDepth(vr) >= 20 & (altDepth(vr) / totalDepth(vr) >= 0.8) & rowSums(softFilterMatrix(vr))==6" filterVars(args, filter, varcaller="gatk", organism="A. thaliana") writeTargetsout(x=args, file="targets_gatk_filtered.txt") ## Filtering of VCF files generated by BCFtools args <- systemArgs(sysma="filter_sambcf.param", mytargets="targets_sambcf.txt") filter <- "rowSums(vr) >= 2 & (rowSums(vr[,3:4])/rowSums(vr[,1:4]) >= 0.8)" # filter <- "rowSums(vr) >= 20 & (rowSums(vr[,3:4])/rowSums(vr[,1:4]) >= 0.8)" filterVars(args, filter, varcaller="bcftools", organism="A. thaliana") writeTargetsout(x=args, file="targets_sambcf_filtered.txt") ## Annotate filtered variants from GATK args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt") txdb <- loadDb("./data/tair10.sqlite") fa <- FaFile(systemPipeR::reference(args)) variantReport(args=args, txdb=txdb, fa=fa, organism="A. thaliana") ## Annotate filtered variants from BCFtools args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt") txdb <- loadDb("./data/tair10.sqlite") fa <- FaFile(systemPipeR::reference(args)) variantReport(args=args, txdb=txdb, fa=fa, organism="A. thaliana") ## Combine results from GATK args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt") combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous")) write.table(combineDF, "./results/combineDF_nonsyn_gatk.xls", quote=FALSE, row.names=FALSE, sep="\t") ## Combine results from BCFtools args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt") combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous")) write.table(combineDF, "./results/combineDF_nonsyn_sambcf.xls", quote=FALSE, row.names=FALSE, sep="\t") ## Summary for GATK args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt") write.table(varSummary(args), "./results/variantStats_gatk.xls", quote=FALSE, col.names = NA, sep="\t") ## Summary for BCFtools args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt") write.table(varSummary(args), "./results/variantStats_sambcf.xls", quote=FALSE, col.names = NA, sep="\t") ## Venn diagram of variants args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt") varlist <- sapply(names(outpaths(args))[1:4], function(x) as.character(read.delim(outpaths(args)[x])$VARID)) vennset_gatk <- overLapper(varlist, type="vennsets") args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt") varlist <- sapply(names(outpaths(args))[1:4], function(x) as.character(read.delim(outpaths(args)[x])$VARID)) vennset_bcf <- overLapper(varlist, type="vennsets") vennPlot(list(vennset_gatk, vennset_bcf), mymain="", mysub="GATK: red; BCFtools: blue", colmode=2, ccol=c("blue", "red")) ## End(Not run)