run_GATK_JointGenotype: '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_GATK_JointGenotype(gvcf, outvcf,
  ref.fa = "~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
  gatkpwd = "$HOME/bin/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar",
  includeNonVariantSites = FALSE, hardfilter = TRUE,
  snpflt = "\"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\"",
  indelflt = "\"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0\"",
  email = NULL, runinfo = c(FALSE, "bigmemh", 1))

set_hardfilter(outvcf, gatkpwd, snpflt, indelflt, ref.fa, runinfo, shid)

Arguments

gvcf	A vector of g.vcf files.
outvcf	File name of the output vcf files, default="mysamples.vcf".
ref.fa	The full path of genome with bwa indexed reference fasta file.
gatkpwd	The absolute path of GenomeAnalysisTK.jar.
includeNonVariantSites	Include loci found to be non-variant after genotyping (for GenotypeGVCFs).
hardfilter	Whether to filter variants. see detail about how to apply hard filters to a call set. https://www.broadinstitute.org/gatk/guide/article?id=2806
snpflt	Parameters to apply the filter to the SNP call set.
indelflt	Parameters to apply the filter to the Indel call set.
email	Your email address that farm will email to once the job was 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.

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

gvcf <- c("1.vcf", "2.vcf")
outvcf <- "out.vcf"
run_GATK_JointGenotype(
gvcf,
outvcf="mysamples.vcf",
ref.fa="~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
gatkpwd="$HOME/bin/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar",
includeNonVariantSites=FALSE,
hardfilter=TRUE,
snpflt="\"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\"",
indelflt="\"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0\"",
email=NULL,
runinfo = c(FALSE, "bigmemh", 1) )

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