run_ANGSD: 'Run ANGSD on farm'

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

Description

angsd

Usage

run_ANGSD(type = "GL", shfile = "slurm-script/run_angsd_cmd.sh",
  bamlist = "list.txt", outfile = "out", ref = "ref.fa", nInd = 20,
  minInd = 10, indF = "indF.txt", anc = "ref.fa", r, email = NULL,
  runinfo = c(FALSE, "bigmemh", 1))

Arguments

r	Chr regions.
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.
inputdf	An input data.frame.
minQ	Minimum base quality score.
minMapQ	[int]=0 Minimum mapQ quality.

Details

see more detail about ANGSD http://popgen.dk/angsd/index.php/Main_Page

Scripts learned from Tim's paper https://github.com/timbeissinger/Maize-Teo-Scripts

Value

return a batch of shell scripts.

Examples

run_ANGSD(type="GL", shfile="slurm-script/run_angsd_cmd.sh",
bamlist="list.txt", outfile="out", ref="ref.fa", nInd=20, minInd=10,
indF="indF.txt", anc="ref.fa",
email=NULL, runinfo = c(FALSE, "bigmemh", 1)

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