Generate all possible combinations between phased haploblocks.
Download the repository from github
git clone https://github.com/LUMC/haploblock-combiner.gitInstall and activate the conda environment.
conda env create --file environment.yml
conda activate haploblock-combinerThere are three levels where configuration options are set, in decreasing order of priority.
- Flags passed to snakemake using
--config, or in the specified--configfile. - Setting specified in the PEP project configuration, under the key
haploblock-combiner - The default settings for the pipeline, as specified in the
common.smkfile
| 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 |
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.
- Only VCF files phased by WhatsHap are currently supported.
- Only VCF files that are compressed with bgzip and indexe with tabix are currently supported