run_alphaimpute: 'Run GATK Joint Genotype on farm'

In yangjl/farmeR: Generate pipelines for maize Genomic and Genetic analysis

Description

GATK Best Practices: recommended workflows for variant discovery analysis.

Usage

run_alphaimpute(pedfile = "data/Parentage_for_imputeR.csv", geno,
  outputdir = "largedata/teo_alpha",
  EditingParameters = "95.0,2.0,98.0,AllSnpOut", RestartOption = 1,
  email = NULL, runinfo = c(FALSE, "bigmemh", 4))

set_alphaimpute(ped, chrgeno, numsnp, EditingParameters, RestartOption, runinfo,
  shid)

Arguments

email	Your email address that farm will email to once the job was done/failed.
fq	An input data.frame for fastq files. Must contains fq1, fq2 and out.
kitpath	The absolute or relative path of the fermi.kit directory that can invoke the pipeline.
genome	The full path of genome with bwa indexed reference fasta file.
s	Approximate genome size, default=3g.
t	Number of threads, default=16.
l	Primary read length, default=100.
arrayjobs	A character specify the number of array you try to run, i.e. 1-100.
jobid	The job name show up in your sq NAME column.

Details

see more detail about GATK: https://www.broadinstitute.org/gatk/guide/bp_step.php?p=1

local programs: bwa Version: 0.7.5a-r405 picard-tools-2.1.1 GenomeAnalysisTK-3.5/

Value

return a batch of shell scripts.

Examples

fq <- data.frame(fq1="fq_1.fq", fq2="f1_2.fq", out="mysample",
                 group="g1", sample="s1",PL="illumina", LB="lib1", PU="unit1")
run_fermikit(fq, kitpath="/home/jolyang/bin/fermikit/",
genome="/home/jolyang/dbcenter/AGP/AGPv2", s='3g', t=16, l=100, arrayjobs="1-2",
jobid="fermi", email=NULL)

yangjl/farmeR documentation built on May 4, 2019, 2:28 p.m.