haploblock-combiner

Generate all possible combinations between phased haploblocks.

Installation

Download the repository from github

git clone https://github.com/LUMC/haploblock-combiner.git

Install and activate the conda environment.

conda env create --file environment.yml
conda activate haploblock-combiner

Settings

There are three levels where configuration options are set, in decreasing order of priority.

1. Flags passed to snakemake using --config, or in the specified --configfile.
2. Setting specified in the PEP project configuration, under the key haploblock-combiner
3. The default settings for the pipeline, as specified in the common.smk file

Setting	Required	Default	Description
pepfile	yes	None	PEP project configuration file
reference	yes	None	Reference file, must match the VCF
region	no	None	Region of the VCF to act on
max_blocks	no	11	Limit on the number of phase blocks

Usage

The following settings are required: --config pepfile=pepfile.yml reference=/path/to/ref.fa region=chrM

Note: Please make sure to specify as small a region as possible. This pipeline will generate 2^(n-1) files, where n is determined by the number of phase sets in the input VCF. So for an unphased VCF with 20 heterozygous variants, it will generate over 1 million files.

Limitations

• Only VCF files phased by WhatsHap are currently supported.
• Only VCF files that are compressed with bgzip and indexe with tabix are currently supported