besenbacher / pooha

POOHA - Parent Of Origin Haplotype Annotator

POOHA

POOHA: Parent Of Origin Haplotype Annotator --- Assign parent of origin to heterozygous variants in a child using read-backed phasing

Installation

To run the POOHA python script you need to have to have python3 with the pysam and pyvcf libraries installed. This can be installed using conda by creating a new environment using the environment.yml file:

conda env create -f environment.yml

To activate this new environment, use:

conda activate pooha

Usage

You can see the options of the POOHA program using the -h option:

./POOHA -h

To identify all new mutations in a parent-offspring trio and assign parental origin to as many of them as possible run:

./POOHA {vcf_file} {father} {mother} {child} {child_bam_file}

Where {fater} {mother} and {child} should be the names given to those individuals in the vcf-file header.

pooha's Issues

P for paternal ?

If the denovo mutation sites signed "P", is it means paternal orign mutation? And "M" means maternal mutations ?