MCHap

MCHap is suite of command line tools for micro-haplotype assembly and genotype calling in autopolyploids. The primary components of MCHap are mchap assemble and mchap call.

Installation

MCHap and it's dependencies can be installed from source using pip. From the root directory of this repository run:

pip install -r requirements.txt
python setup.py sdist
pip install dist/mchap-*.tar.gz

You should then be able to use the command line tool mchap which is a wrapper around mchap assemble and mchap call.

MCHap includes a suite of unit tests which can be run from the root directory of this repository with:

pytest -v ./

MCHap assemble

mchap assemble is used for de novo assembly of micro-haplotypes in one or more individuals. Haplotypes are assembled from aligned reads in BAM files using known SNVs (single nucleotide variants) from a VCF file. A BED file is also required to specify the assembled loci. The output of mchap assemble is a VCF file with assembled micro-haplotype variants and genotype calls (some genotype calls may be incomplete). See the MCHap assemble documentation for further information..

MCHap call

mchap call is used for (re-) calling genotypes using a set of known micro-haplotypes. Genotypes are called using aligned reads in BAM files and known micro-haplotype alleles from a VCF file. The output of mchap call is a VCF file with micro-haplotype variants and genotype calls (all genotype calls will be complete). It is often beneficial to re-call genotypes with mchap call using the micro-haplotypes reported by mchap assemble, particularly in populations of related samples. See the MCHap call documentation for further information.

MCHap find-snvs

mchap find-snvs is a simple tool for identifying putative SNVs to use as the basis for haplotype assembly. Putative SNVs are identified based on minimum thresholds for allele depths and/or frequencies estimated from depths. The output is reported as a simple VCF file which includes allele depths and population allele frequencies (estimated from the mean of individual frequencies), but no genotype calls.

Example notebook

See the example notebook demonstrating genotype calling with MCHap in a bi-parental population.

Experimental features

⚠️ WARNING: The following tools are highly experimental!!! ⚠️

• mchap call-pedigree: for pedigree informed genotype calling.
• mchap atomize: for converting micro-haplotype calls to phased sets of SNVs.

See the experimental notebook demonstrating the call-pedigree tool as presented at the 2024 Tools for Polyploids workshop.

Funding

The development of MCHap was partially funded by the "Tools for Polyploids" Specialty Crop Research Initiative (NIFA USDA SCRI Award # 2020-51181-32156).