haplotyper: a wrapper around gatk haplotyper

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

Description

a wrapper around gatk haplotyper

Usage

haplotyper(x, samplename = opts_flow$get("samplename"), outfile,
  split_by_chr = TRUE, ref_fasta = opts_flow$get("ref_fasta"),
  java_exe = opts_flow$get("java_exe"),
  java_mem = opts_flow$get("java_mem"),
  java_tmp = opts_flow$get("java_tmp"),
  gatk_jar = opts_flow$get("gatk_jar"),
  haplotyper_opts = opts_flow$get("haplotyper_opts"),
  cpu_haplotyper = opts_flow$get("cpu_haplotyper"))

Arguments

x

input bam

Details

For more details refer to: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_CatVariants.php

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