consHap (v0.1): Majority voting approach to construct consensus haplotype estimator from multiple phased haplotypes.

Licence

Copyright 2020 Ziad Al Bkhetan

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Prerequisites

1. Python 3.5.2 or later.

Commands

Help

python3 consHap.py --help

Consensus haplotype construction

python3 consHap.py -CONS -O path_output_file_prefix -F list_of_input_files 

You can use the option -GZ for gzipped input and output files.
You can use the option -RI to impute missing SNPs as the reference file (first file in the provided list).

Convert SHAPEIT format haplotypes to VCF

 python3 consHap.py -C2V -O path_output_file_prefix -SF path_input_file_prefix

You can use the option -GZ for gzipped input and output files.
Details about SHAPEIT format are available here: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample.

Convert EIGENSTRAT format to SHAPEIT format

 python3 consHap.py -C2S -O path_output_file_prefix -HF path_input_file_prefix

You can use the option -GZ for gzipped input and output files.
Details about EIGENSTRAT format are available here: https://reich.hms.harvard.edu/software/InputFileFormats.

Citation

If you use consHap in a published study, please mention the version of the tool and cite at least one of these articles:

Al Bkhetan, Ziad, et al. "Exploring effective approaches for haplotype block phasing." BMC bioinformatics 20.1 (2019): 540.

Al Bkhetan, Ziad, et al. "Evaluation of consensus strategies for haplotype phasing." Briefings in bioinformatics: bbaa280

Contact information

For any help or inquiries, please contact: ziad.albkhetan@gmail.com.