consHap (v0.1): Majority voting approach to construct consensus haplotype estimator from multiple phased haplotypes.
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.
- Python 3.5.2 or later.
python3 consHap.py --help
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).
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.
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.
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
For any help or inquiries, please contact: ziad.albkhetan@gmail.com.