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 ofvcfbreakmulti
,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