Installation of PHASEfilter

Regular Install

Install directly with pip:

1$ pip3 install phasefilter

Important

When install ‘pyvcf’, dependent package, and if your setuptools>=58 it goes to throw an error: “error in PyVCF setup command: use_2to3 is invalid.” Please, use setuptools<58. Setuptools>=58 breaks support for use_2to3 thats why you are facing this error for the package ‘pyvcf’.

PHASEfilter in a virtual environment

Install with virtual environment:

1$ virtualenv phasefilter --python=python3 --prompt "(phasefilter) "
2$ source phasefilter/bin/activate
3(phasefilter) $ pip3 install phasefilter
4### OR if you want to run the tests
5(phasefilter) $ pip3 install phasefilter --install-option test

Important

When install ‘pyvcf’, dependent package, and if your setuptools>=58 if goes to throw an error: “error in PyVCF setup command: use_2to3 is invalid.” Please, use setuptools<58. Setuptools>=58 breaks support for use_2to3 thats why you are facing this error.

After that you have five scripts available:

1$ phasefilter
2$ phasefilter_single
3$ make_alignment
4$ reference_statistics
5$ synchronize_genomes

Dependecies

PHASEfilter relies on several bioinformatic software to run:

  • minimap2 >= 2.22

  • samtools >= 1.3

  • bcftools >= 1.3

  • htslib >= 1.3

  • bgzip >= 1.3