gatk.haplotypecaller: gatk.haplotypecaller

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

Description

A wrapper function to run GATK (HaplotypeCaller)

Usage

gatk.haplotypecaller(fns.bam, output.dir, sample.name, ref.fa, genotyping_mode="DISCOVERY", output_mode="EMIT_VARIANTS_ONLY", stand_call_conf_number=30, unsafe=FALSE, run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to BAM files
output.dir	Output directory
sample.name	A character vector for the sample names
ref.fa	Referance fasta file
genotyping_mode	A parameter value for –genotyping_mode in GATK. A character vector to determine the alternate alleles to use for genotyping (default: DISCOVERY)
output_mode	A parameter value for –output_mode in GATK. A character vector to produces variant calls (default: EMIT_VARIANTS_ONLY)
stand_call_conf_number	A parameter value for -stand_call_conf in GATK. A numeric value of The minimum phred-scaled confidence threshold at which variants should be called (default: 30)
unsafe	A parameter value for -U ALLOW_N_CIGAR_READS in GATK. This parameter must be TRUE in RNA-seq data.
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.

Details

HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region.

Value

Variant calling format files (.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.