preprocess: Pre-process bam files following Broad's best practices for...

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

Description

This function provides a wrapper around the best practices described on GATK's website. If the link is broken google 'GATK best practices'

This aims to perform the following steps ( for DNA ):

• mark duplicates

• realign indels

• recalibrate bases

• current version: 3.4-46

For RNA GATK recommends a additional step of split n trim, which is not currently supported (contributions welcome !).

NOTE:

Some GATK tools use CPU threads while others use data threads, flowr tries to use efficiently make the best use of both/either depending on tool's compatibility.

Usage

preprocess(x, outfile, samplename = opts_flow$get("samplename"),
  split_by_chr = opts_flow$get("split_by_chr"),
  java_exe = opts_flow$get("java_exe"),
  java_tmp = opts_flow$get("java_tmp"),
  gatk_jar = opts_flow$get("gatk_jar"),
  picard_dir = opts_flow$get("picard_dir"),
  samtools_exe = opts_flow$get("samtools_exe"), cpu_markdup = 1,
  mem_markdup = "-Xmx8g", cpu_target = opts_flow$get("cpu_target"),
  mem_target = "-Xmx32g", cpu_realign = opts_flow$get("cpu_realign"),
  mem_realign = "-Xmx4g",
  cpu_baserecalib = opts_flow$get("cpu_baserecalib"),
  mem_baserecalib = "-Xmx4g",
  cpu_printreads = opts_flow$get("cpu_printreads"),
  mem_printreads = "-Xmx4g", ref_fasta = opts_flow$get("ref_fasta"),
  gatk_target_opts = opts_flow$get("gatk_target_opts"),
  gatk_realign_opts = opts_flow$get("gatk_realign_opts"),
  gatk_baserecalib_opts = opts_flow$get("gatk_baserecalib_opts"),
  gatk_printreads_opts = opts_flow$get("gatk_printreads_opts"))

Arguments

java_exe	path to java
java_tmp	path to java tmp, can leave blank
cpu_markdup	not used.
cpu_target	number of threads used for GATK target creation step
q_obj	is provided output is a flow object, else a list of commands to run
java_mem_markdup	memory provided to java

Details

Flow following Broad's best practices for variant calling, starting from sorted bam

Examples

## Not run: 
## load options, including paths to tools and other parameters
load_opts(fetch_conf("ngsflows.conf"), check = FALSE)
out = bam_preprocess("my_wex.bam", samplename = "samp", split_by_chr = TRUE)


## End(Not run)

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