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Installation
You can install vcfMerger2 in three ways:
-
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}
-
clone the repository and add the bin directory to your
PATH
as described above. -
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
- linux system
- not tested on MacOSx
- not windows-compatible
All the following tools must be in your PATH
before running vcfMerger2
scripts
- grep
- awk
- echo
- find
- sed
- xxd
- 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)
Enumeration of the python modules' used while testing vcfMerger2 (associated version in parenthesis)
- 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)
- collections
- getopt
- gzip
- shutil
- subprocess
- sys, os, time, re
- warnings
- 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)