gatk.variantfilter: gatk.variantfilter

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run GATK (VariantFiltration)

Usage

gatk.variantfilter(fns.vcf, output.dir, sample.name, ref.fa, FS=30.0, QD=2.0, QUAL=50, DP=5, gatk.window=35, cluster=3, run.cmd=TRUE, mc.cores=1)

Arguments

fns.vcf	Path to VCF files
output.dir	Output directory
ref.fa	Reference fasta file
FS	A parameter value for FS in GATK. FisherStrand. (default=30.0)
QD	A parameter value for QD in GATK. Quality by Depth. (default=2.0)
QUAL	A parameter value for QUAL in GATK. Low quality. (default=50)
DP	A parameter value for DP in GATK. Low depth. (default=5)
gatk.window	A parameter value for -window in GATK. The window size (in bases) in which to evaluate clustered SNPs.
cluster	A parameter value for -cluster in GATK. The number of SNPs which make up a cluster. Must be at least 2.
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.
sample.name	A character vector for the sample names

Details

Filter variant calls based on INFO and/or FORMAT annotations. This tool is designed for hard-filtering variant calls based on certain criteria.

Value

Filtered VCF file (eg. .f.vcf)

References

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

See Also

https://software.broadinstitute.org/gatk/

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.