simp: 'Simulate phenotype'

In yangjl/quantgen: R package for basic quantgen simulation and/or modeling.

Description

simulate QTL effect and phentoype.

Usage

simp(X, h2, alpha, NQTN, distribution, a2 = 0)

Arguments

h2	The full path of genome with bwa indexed reference fasta file.
inputdf	An input data.frame for fastq files. Must contains fq1, fq2, out (and/or bam). If inputdf contained bam, bwa alignment will be escaped. Additional columns: group (group id), sample (sample id), PL (platform, i.e. illumina), LB (library id), PU (unit, i.e. unit1). These strings (or info) will pass to BWA mem through -R.
gatkpwd	The absolute path of GenomeAnalysisTK.jar.
picardpwd	The absolute path of picard.jar.
minscore	Minimum score to output, default=5, [bwa 30]. It will pass to bwa mem -T INT.
markDup	Mark Duplicates, default=TRUE.
addRG	Add or replace Read Groups using Picard AddOrReplaceReadGroups, default=FALSE.
realignInDels	Realign Indels, default=FALSE. IF TRUE, a golden indel.vcf file should be provided.
indels.vcf	The full path of indels.vcf.
recalBases	Recalibrate Bases, default=FALSE. IF TRUE, a golden snps.vcf file should be provided.
dbsnp.vcf	The full path of dbsnp.vcf.
email	Your email address that farm will email to once the jobs were done/failed.
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE 2) -p partition name, default=bigmemh and 3) –cpus, default=1. It will pass to set_array_job.

Value

return a batch of shell scripts.

Examples

inputdf <- data.frame(fq1="fq_1.fq", fq2="f1_2.fq", out="mysample",
                 group="g1", sample="s1", PL="illumina", LB="lib1", PU="unit1")

run_GATK(inputdf,
         ref.fa="~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
         gatkpwd="$HOME/bin/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar",
         picardpwd="$HOME/bin/picard-tools-2.1.1/picard.jar",
         markDup=TRUE,
         realignInDels=FALSE, indels.vcf="indels.vcf",
         recalBases=FALSE, dbsnp.vcf="dbsnp.vcf",
         email=NULL, runinfo = c(FALSE, "bigmemh", 1))

yangjl/quantgen documentation built on May 4, 2019, 2:29 p.m.