dedupCNV: run the picard and GATK pre processing steps on bam...

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

Description

run the picard and GATK pre processing steps on bam alignments

Usage

dedupCNV(inBAM, projName, refGenome, gatkStep = T,
  tmpDir = file.path("/scratch/pschofield/Projects", projName, "tmp"),
  picardDir = "/apps/modules/pkg/apps/picardtools/1.96/noarch",
  gatkDir = "/apps/modules/pkg/apps/gatk/3.1.1/noarch",
  javaMod = "compilers/java/1.7.0_80/noarch",
  gatkMod = "apps/gatk/3.1.1/noarch",
  picardMod = "apps/picardtools/1.96/noarch",
  samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7",
  gatkRes = "/data/compbio/hsleong/Genome/gatk/hg19/bundle",
  ncores = 1, scpIt = T, noSub = F)

Arguments

filename

merged bam file

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