filterVars: Filter VCF files

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

Filter VCF files

Description

Convenience function for filtering VCF files based on user definable quality parameters. The function imports each VCF file into R, applies the filtering on an internally generated VRanges object and then writes the results to a new VCF file.

Usage

filterVars(files, filter, varcaller="gatk", organism,
            out_dir="results")

Arguments

files	named character vector with paths of the input VCF files.
filter	Character vector of length one specifying the filter syntax that will be applied to the internally created VRanges object.
varcaller	Character vector of length one specifying the variant caller used for generating the input VCFs. Currently, this argument can be assigned 'gatk', 'bcftools' or 'vartools'.
organism	Character vector specifying the organism name of the reference genome.
out_dir	Character vector of a results directory name. Default is results.

Value

Output files in VCF format. Their paths can be obtained with outpaths(args) or output(args).

Author(s)

Thomas Girke

See Also

variantReport combineVarReports, varSummar

Examples

## 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: 
library(VariantAnnotation)
system("bwa index -a bwtsw ./data/tair10.fasta")
bampaths <- runCommandline(args=args)

## Alignment with BWA (parallelized on compute cluster)
resources <- list(walltime="20:00:00", nodes=paste0("1:ppn=", cores(args)), memory="10gb")
reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.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="20:00:00", nodes=paste0("1:ppn=", 1), memory="10gb")
reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.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="20:00:00", nodes=paste0("1:ppn=", 1), memory="10gb")
reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.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)

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.