Description Usage Arguments Details Value Examples
GATK Best Practices: recommended workflows for variant discovery analysis.
1 2 3 4 5 6 7 | 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)
|
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. |
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 | 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)
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