Description Usage Arguments Details Value Examples
View source: R/run_GATK_JointGenotype.R
GATK Best Practices: recommended workflows for variant discovery analysis.
1 2 3 4 5 6 7 8 9 | run_GATK_JointGenotype(gvcf, outvcf,
ref.fa = "~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
gatkpwd = "$HOME/bin/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar",
includeNonVariantSites = FALSE, hardfilter = TRUE,
snpflt = "\"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\"",
indelflt = "\"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0\"",
email = NULL, runinfo = c(FALSE, "bigmemh", 1))
set_hardfilter(outvcf, gatkpwd, snpflt, indelflt, ref.fa, runinfo, shid)
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gvcf |
A vector of g.vcf files. |
outvcf |
File name of the output vcf files, default="mysamples.vcf". |
ref.fa |
The full path of genome with bwa indexed reference fasta file. |
gatkpwd |
The absolute path of GenomeAnalysisTK.jar. |
includeNonVariantSites |
Include loci found to be non-variant after genotyping (for GenotypeGVCFs). |
hardfilter |
Whether to filter variants. see detail about how to apply hard filters to a call set. https://www.broadinstitute.org/gatk/guide/article?id=2806 |
snpflt |
Parameters to apply the filter to the SNP call set. |
indelflt |
Parameters to apply the filter to the Indel call set. |
email |
Your email address that farm will email to once the job was done/failed. |
runinfo |
Parameters specify the array job partition information.
A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE
2) -p partition name, default=bigmemh and 3) –cpus, default=1.
It will pass to |
see more detail about GATK: https://www.broadinstitute.org/gatk/guide/bp_step.php?p=1
local programs: bwa Version: 0.7.5a-r405 picard-tools-2.1.1 GenomeAnalysisTK-3.5/
return a batch of shell scripts.
1 2 3 4 5 6 7 8 9 10 11 12 13 | gvcf <- c("1.vcf", "2.vcf")
outvcf <- "out.vcf"
run_GATK_JointGenotype(
gvcf,
outvcf="mysamples.vcf",
ref.fa="~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
gatkpwd="$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) )
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