randomly permute the locations of variants in a vcf

In order to perform a permutations test on a set of variants, you first need to permute the locations of the variants a bunch of times. This program does just that: it takes as input a VCF file containing the actual locations of variants and outputs a set of randomized versions of the VCF file, each containing the same variants but in random positions.

Due to a bug in pyvcf, this package only supports python 3.9 and 3.10 at the moment. That bug should be fixed in the next release of pyvcf3, but in the meantime, you'll need to make a python3.9 environment. So to install:

conda create -n permute-vcf python=3.9
conda activate permute-vcf
git clone https://github.com/WarrenLab/permute-vcf.git
cd permute-vcf
pip install .

To create 10 permutations of a vcf file test.vcf.gz and write them to the permutations/ subdirectory, you can run a command like this:

permute-vcf -n 10 -o permutations/ test.vcf.gz

After that, your output directory will have files 0.vcf.gz through 9.vcf.gz, each containing a different permutation of the input data.

The help dialog for the program has more details about parameters etc.