Installation

Installation

How to Install vcfMerger2

You can install vcfMerger2 in three ways:

1. download the git repository as a compressed archived, uncompressed and untar the archive, and update your PATH with the command
   export PATH=/install_directory/vcfMerger2/bin/:${PATH}

2. clone the repository and add the bin directory to your PATH as described above.

3. clone a specific release version of vcfMerger2, such as for instance for the version 0.5.0-beta, the following command:
   git clone [email protected]:tgen/vcfMerger2.git --release 0.6.1-beta
   or
   git clone https://github.com/tgen/vcfMerger2.git --release 0.6.1-beta

vcfMerger2 requirements

Operating System Compatible

• linux system
• not tested on MacOSx
• not windows-compatible

Dependencies

All the following tools must be in your PATH before running vcfMerger2 scripts

Shell

• grep
• awk
• echo
• find
• sed
• xxd

Python

• python 3.6.0 or up

we only tested our vcfMerger2 tool with version 3.6.0 of Python; feedback appreciated if you have successfully used a different version of Python along with a different newer version of the python modules)

Python Modules

Enumeration of the python modules' used while testing vcfMerger2 (associated version in parenthesis)

non Built-in

- cyvcf2 (0.8.4)
- intervene (0.6.4) [implies you also must install R packages UpSetR (tested with version v1.3.3) ]
- argparse (1.1)
- json (2.0.9)
- logging (0.5.1.2)
- Pillow (6.0.0)
- natsort (5.0.3)

Built-in

- collections
- getopt
- gzip
- shutil
- subprocess
- sys, os, time, re 
- warnings

Other Tools

• samtools 1.7 or up (tested with 1.7 and 1.9)
• bcftools 1.7 or up (tested with 1.7 and 1.9)
• bedtools 2.26.0 or up (tested with 2.26.0)
• vt v0.57721 or up (tests done with v0.57721)
• snpSift 4.3t or up (snpSift.jar ; tested with 4.2 and 4.3t)
• phASER v1.1.1 or up (test done with v1.1.1)

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