run_fastCall: 'Run fastCall on farm'

Description Usage Arguments Details Value Examples

Description

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

Usage

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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

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