run_fastCall: 'Run fastCall on farm'

In yangjl/farmeR: Generate pipelines for maize Genomic and Genetic analysis

Description

Super fast variant caller for whole genome shotgun (WGS) sequencing data. It works for diploid species, including both inbreds and outcrossers.

Usage

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))

Arguments

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 set_array_job.

Details

see more details: https://github.com/Fei-Lu/FastCall

Prerequisites: module load java/1.8 Samtools

Value

return a batch of shell scripts.

Examples

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))

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