├── .gitignore ├── 00_archive ├── .gitignore └── TODO.md ├── 01_scripts ├── .gitignore ├── 00_validate_project.sh ├── 01_extract_positions.sh ├── 02_fasta_extract_flanking_regions.py ├── 03_map_reads.sh ├── 04_extract_features_from_alignments.py ├── 05_explore_features.R ├── 06_score_markers.py ├── 07_correspondence.py ├── 08_replace_coordinates_in_vcf.py └── util │ ├── benchmark_format_data.sh │ ├── benchmark_get_elapsed_time.py │ ├── cleanup_intermediate_files.sh │ ├── collinearity.sh │ ├── count_unique_lines.py │ ├── find_position_correction.py │ ├── get_test_dataset.sh │ ├── run_test.sh │ ├── split_positions.py │ ├── subsample_vcf.py │ └── validate_sequence_names.py ├── 02_infos ├── .gitignore ├── snplift_config.sh └── test_config.sh ├── 03_genomes └── .gitignore ├── 04_input_vcf └── .gitignore ├── 05_collinearity └── .gitignore ├── 06_liftover └── .gitignore ├── 99_logfiles └── .gitignore ├── README.md └── snplift /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/.gitignore -------------------------------------------------------------------------------- /00_archive/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /00_archive/TODO.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/00_archive/TODO.md -------------------------------------------------------------------------------- /01_scripts/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /01_scripts/00_validate_project.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/00_validate_project.sh -------------------------------------------------------------------------------- /01_scripts/01_extract_positions.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/01_extract_positions.sh -------------------------------------------------------------------------------- /01_scripts/02_fasta_extract_flanking_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/02_fasta_extract_flanking_regions.py -------------------------------------------------------------------------------- /01_scripts/03_map_reads.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/03_map_reads.sh -------------------------------------------------------------------------------- /01_scripts/04_extract_features_from_alignments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/04_extract_features_from_alignments.py -------------------------------------------------------------------------------- /01_scripts/05_explore_features.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/05_explore_features.R -------------------------------------------------------------------------------- /01_scripts/06_score_markers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/06_score_markers.py -------------------------------------------------------------------------------- /01_scripts/07_correspondence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/07_correspondence.py -------------------------------------------------------------------------------- /01_scripts/08_replace_coordinates_in_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/08_replace_coordinates_in_vcf.py -------------------------------------------------------------------------------- /01_scripts/util/benchmark_format_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/benchmark_format_data.sh -------------------------------------------------------------------------------- /01_scripts/util/benchmark_get_elapsed_time.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/benchmark_get_elapsed_time.py -------------------------------------------------------------------------------- /01_scripts/util/cleanup_intermediate_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/cleanup_intermediate_files.sh -------------------------------------------------------------------------------- /01_scripts/util/collinearity.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/collinearity.sh -------------------------------------------------------------------------------- /01_scripts/util/count_unique_lines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/count_unique_lines.py -------------------------------------------------------------------------------- /01_scripts/util/find_position_correction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/find_position_correction.py -------------------------------------------------------------------------------- /01_scripts/util/get_test_dataset.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/get_test_dataset.sh -------------------------------------------------------------------------------- /01_scripts/util/run_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/run_test.sh -------------------------------------------------------------------------------- /01_scripts/util/split_positions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/split_positions.py -------------------------------------------------------------------------------- /01_scripts/util/subsample_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/subsample_vcf.py -------------------------------------------------------------------------------- /01_scripts/util/validate_sequence_names.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/01_scripts/util/validate_sequence_names.py -------------------------------------------------------------------------------- /02_infos/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /02_infos/snplift_config.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/02_infos/snplift_config.sh -------------------------------------------------------------------------------- /02_infos/test_config.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/02_infos/test_config.sh -------------------------------------------------------------------------------- /03_genomes/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /04_input_vcf/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /05_collinearity/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /06_liftover/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /99_logfiles/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/README.md -------------------------------------------------------------------------------- /snplift: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enormandeau/snplift/HEAD/snplift --------------------------------------------------------------------------------