gatk.baserecalibrator: gatk.baserecalibrator

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

Description

A wrapper function to run GATK (BaseRecalibrator)

Usage

gatk.baserecalibrator(fns.bam, output.dir, sample.name, ref.fa, ref.dbSNP, ref.gold_indels, unsafe=FALSE, run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to input BAM files
output.dir	Output directory
sample.name	A character vector for the sample names
ref.fa	Reference fasta file
ref.dbSNP	Known SNP sites reference(VCF)
ref.gold_indels	Known sites to indel variant call format(VCF)
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

First pass of the base quality score recalibration. Generates a recalibration table based on various covariates. The default covariates are read group, reported quality score, machine cycle, and nucleotide context. This walker generates tables based on specified covariates via by-locus traversal operating only at sites that are in the known sites VCF.

Value

GATK report file contained recalibration table by read group, quality scores and all the optional covariates. (e.g., .grp)

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.