picard_reorder: Use picard's MergeSamFiles tool to merge bam/sam files

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

Description

The resulting file is sorted and index is created for it. Validation stringency of inputs is kept as lenient. Multi-threading is turned on by default, though in our experience this does not seem to use a lot of threads.

Usage

picard_reorder(x, outfile, samplename = opts_flow$get("samplename"),
  java_exe = opts_flow$get("java_exe"),
  java_mem = opts_flow$get("java_mem"),
  java_tmp = opts_flow$get("java_tmp"),
  picard_dir = opts_flow$get("picard_dir"),
  picard_reorder_opts = opts_flow$get("picard_reorder_opts"),
  ref_fasta = opts_flow$get("ref_fasta"),
  samtools_exe = opts_flow$get("samtools_exe"))

Arguments

x	a vectors of files to merge
picard_dir

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.