run_bs2vcf: 'Run bs2vcf job on farm'

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

Description

convert BSMAP format to VCF format Find help about 'bs2vcf -h'. bs2vcf -p /group/jrigrp4/BS_teo20/BSMAP_output -i test_methratio.txt -o test_methratio.vcf

Usage

run_bs2vcf(inputdf, email = NULL, runinfo = c(FALSE, "bigmemh", 1))

Arguments

inputdf	An input data.frame for fastq files. Must contains bsmap and out.
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.

Value

return a batch of shell scripts.

Examples

inputdf <- data.frame(bsmap="test_ratio.txt", out="test_ratio.vcf")
run_bs2vcf( inputdf, email=NULL, runinfo = c(FALSE, "bigmemh", 1))

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