Installation

Required tools

  • GATK >= 4.0 ( java 8 required )
  • Bedtools

  • Python 2.7

    -scipy

    -numpy

    -multiprocessing

  • R

    -ztable

    -rmarkdown

    -corrplot

Installation with ‘git clone’

First, clone the repository.

$ git clone https://github.com/heinc1010/BAMixChecker

Installation with the compressed file

Or, download the compressed file from https://github.com/heinc1010/BAMixChecker.

Then, decompress the .zip file.

$ unzip BAMixChecker-master.zip

Set configeration

And then set the tools PATH on the configuration file.

$ cd BAMixChecker
$ vim BAMixChecker.config

GATK=/path/of/gatk
BEDTOOLS=/path/of/bedtools
  • Default (If you added the path in $PATH, you don’t need to modify the configuration file )
GATK=gatk
BEDTOOLS=bedtools