cluster_vcf_records

Python3 package to cluster VCF records.

Used by gramtools and minos - written specifically for those projects and no others.

Dependencies

• vt
• vcflib. Specifically, needs either vcflib, or all three of vcfbreakmulti, vcfallelicprimitives, vcfuniq to be installed and in your $PATH.
• bcftools. This is optional. Only needed if you need to read bcf files.

Install

pypi

pip3 install wheel cluster_vcf_records

conda

conda install -c bioconda cluster_vcf_records

Usage

import cluster_vcf_records

input_vcf_file_paths = ['spam.vcf', 'eggs.vcf']
cluster_vcf_records.cluster(input_vcf_file_paths,
                            'reference.fasta',
                            'clustered_output.vcf')

For further information and a description of optional arguments, see help(cluster_vcf_records.vcf_clusterer.VcfClusterer)

Develop

Run tox (or pytest) from the top-level directory to run all unit tests.

License

MIT