Description Usage Arguments Details Value Examples
Super fast variant caller for whole genome shotgun (WGS) sequencing data. It works for diploid species, including both inbreds and outcrossers.
1 2 3 4 | run_fastCall(ref.fa = "~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
fastCallpwd = "$HOME/bin/fastCall", bamdir = "/",
baminfofile = "taxaBamMap.txt", chr = NULL, outdir = "", email = NULL,
runinfo = c(FALSE, "bigmemh", 1))
|
ref.fa |
The full path of genome with bwa indexed reference fasta file. |
fastCallpwd |
The absolute path of GenomeAnalysisTK.jar. |
bamdir |
The full path of the bam files. |
baminfofile |
Taxa info for bam files, each line contains 1 to N bam files for the taxa. |
chr |
Chr number, i.e. 1, default=NULL, ten chrs will run as 10 array jobs. |
outdir |
The full path of the output files. Note log and shell codes will also put here. |
email |
Your email address that farm will email to once the jobs were done/failed. |
runinfo |
Parameters specify the array job partition information.
A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE
2) -p partition name, default=bigmemh and 3) –cpus, default=1.
It will pass to |
see more details: https://github.com/Fei-Lu/FastCall
Prerequisites: module load java/1.8 Samtools
return a batch of shell scripts.
1 2 3 4 5 6 7 8 | bam <- data.frame(taxa=c("t1", "t2"), bam=c("t1_1.bam", "t2.bam"), bam=c("t1_2.bam", ""))
write.table(bam, "test/taxaBamMap.txt", sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE )
run_fastCall(ref.fa = "~/dbcenter/Ecoli/reference/Ecoli_k12_MG1655.fasta",
fastCallpwd = "$HOME/bin/fastCall", bamdir = "$HOME/test",
baminfofile = "test/taxaBamMap.txt", chr = NULL, outdir = "test",
email = NULL,
runinfo = c(FALSE, "bigmemh", 1))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.