alignBWA: Simple subread aligner

In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions

Description

This is a simpler subread aligner that runs of single fastq files rather than individual lane fastqs from the HiSeq. There maybe QC advantages of aligning the individual fastqc but sometimes it is just simpler to merge before the event.

Usage

alignBWA(fileName, projName, runId, sampleBC = NULL,
  outRoot = file.path("/scratch/pschofield/Projects", projName),
  outName = "Data/alignments/bwa", noSub = F, scpIt = T,
  bwaMod = "apps/bwa/0.7.13/gcc-4.4.7", debugRG = F,
  samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", mem = "32Gb",
  refGenome = NULL, ncores = 8, fqExt = ".fastq", pe = T)

Arguments

projName	project name
outRoot	output root directory
fileList	list of fastq file

PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.