genCNValignmentStats: generate alignments stats for BWA CNV alignments

Description Usage Arguments

View source: R/genCNValignmentStats.R

Description

generate alignments stats for BWA CNV alignments

Usage

1
2
3
4
5
6
genCNValignmentStats(sid, bamDir, fqsDir, projName,
  remRoot = file.path("/scratch/pschofield/Projects", projName),
  outDir = "Analysis/mapping_stats", noSub = F, ncores = 1,
  scpIt = T, mem = "32Gb",
  samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", ufExt = ".bam",
  mdExt = "_dedup.bam", rdExt = "_rmdup.bam")

Arguments

bamDir

directory of alignment files


PietaSchofield/plibb documentation built on Nov. 11, 2018, 5:15 a.m.