Description Usage Arguments Details Value Examples
Fermikit is a de novo assembly based variant calling pipeline for Illumina short reads
1 2 3 4 5 | run_fermikit(fq, kitpath = "$HOME/bin/fermikit", ref.fa = "", s = "2.3g",
l = 100, email = NULL, runinfo = c(FALSE, "bigmemh", 1))
run_fermikit_vcfcall(bamdir = "", kitpath = "$HOME/bin/fermikit",
ref.fa = "", email = NULL, runinfo = c(FALSE, "bigmemh", 1))
|
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. |
ref.fa |
The full path of genome with bwa indexed reference fasta file. |
s |
Approximate genome size, default=2.3g. |
l |
Primary read length, default=100. |
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 |
bamdir |
Path of the bam files. |
see more detail about fermikit by Li, Heng: https://github.com/lh3/fermikit
return a batch of shell scripts.
1 2 3 4 5 6 7 8 | fq <- data.frame(fq1=c("f_1.fq", "t_1.fq"), fq2=c("f_1.fq", "t_2.fq"), out=c("t1", "t2"))
run_fermikit(fq, kitpath="/home/jolyang/bin/fermikit/",
ref.fa="path/to/fastq.fa", s='2.3g', l=100,
email=NULL, runinfo = c(FALSE, "bigmemh", 1)
run_fermikit(bamdir="", kitpath="$HOME/bin/fermikit",
ref.fa="",
email=NULL, runinfo = c(FALSE, "bigmemh", 1))
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